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(-) Description

Title :  HCGC FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  T. Fujishiro, U. Ermler, S. Shima
Date :  11 Aug 15  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Rossmann-Like Fold, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fujishiro, L. Bai, T. Xu, X. Xie, M. Schick, J. Kahnt, M. Rother, X. Hu U. Ermler, S. Shima
Identification Of Hcgc As A Sam-Dependent Pyridinol Methyltransferase In [Fe]-Hydrogenase Cofactor Biosynthesis
Angew. Chem. Int. Ed. Engl. V. 55 9648 2016
PubMed-ID: 27391308  |  Reference-DOI: 10.1002/ANIE.201604352

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0489
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ROSSMANN-LIKE DOMAIN, RESIDUES 1-268
    Gene: MJ0489
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: HCGC

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:35 , ARG A:39 , LYS A:68 , TYR A:69binding site for residue SO4 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D5O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile H:78 -His H:79

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D5O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D5O)

(-) Exons   (0, 0)

(no "Exon" information available for 5D5O)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeee.....eeeehhhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d5o A  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262      
                                                                                             79|                                                                                                                                                                                  
                                                                                              90                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhh.....eeeee...eeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh.hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o B  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDISIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72     || 94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264    
                                                                                            78|                                                                                                                                                                                 
                                                                                             91                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeeee...eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o C  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     
                                                                                             79|                                                                                                                                                                                 
                                                                                              91                                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeeee......eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o D  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        
                                                                                             79|                                                                                                                                                                                    
                                                                                              88                                                                                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeeee.....eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o E  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
                                                                                             79|                                                                                                                                                                                   
                                                                                              89                                                                                                                                                                                   


Chain F from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhh..eeee...eee.hhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh.hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o F  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72     || 95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265   
                                                                                            78|                                                                                                                                                                                
                                                                                             92                                                                                                                                                                                


Chain G from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeeee...eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o G  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263     
                                                                                             79|                                                                                                                                                                                 
                                                                                              91                                                                                                                                                                                 


Chain H from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhh..eeeeeeee......eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh.hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d5o H  13 MVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    22        32        42        52        62        72      ||90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        
                                                                                             79|                                                                                                                                                                                    
                                                                                              88
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5D5O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D5O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D5O)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5D5O)

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  5d5o
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  Y489_METJA | Q57913
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Y489_METJA | Q57913: 5d4t 5d4u 5d4v 5d5t

(-) Related Entries Specified in the PDB File

5d4t 5d4u 5d4v