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(-) Description

Title :  CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096672785533) FROM UNCULTURED MARINE ORGANISM AT 2.20 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  26 Jan 07  (Deposition) - 06 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Ferredoxin-Like Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Hypothetical Protein (Jcvi_pep_1096672785533) From An Environmental Metagenome (Unidentified Marine Microbe), Sorcerer Ii Global Ocean Sampling Experiment At 2. 20 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: UNCULTURED MARINE ORGANISM
    Organism Taxid: 360281
    Other Details: SYNTHETIC GENE: THE GENE PRODUCT WAS BASED ON JCVI_PEP_1096672785533 FROM THE SORCERER II GLOBAL OCEAN SAMPLING EXPERIMENT

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   CD  
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 7)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:36 , TYR A:39 , HOH A:150 , PHE B:112 , GLU F:73 , GLN F:76BINDING SITE FOR RESIDUE EDO A 117
2AC2SOFTWAREASN A:103 , ASN A:104 , ARG A:105 , HOH A:153 , VAL B:55 , TRP B:56 , HOH B:133BINDING SITE FOR RESIDUE EDO A 118
3AC3SOFTWAREASN E:11 , TYR E:69 , TYR E:75 , GLN E:79 , HOH E:121BINDING SITE FOR RESIDUE EDO E 117
4AC4SOFTWAREARG D:41 , ALA D:45 , ILE D:81 , GLU E:80 , ASP E:83BINDING SITE FOR RESIDUE EDO E 118
5AC5SOFTWARETRP D:34 , SER D:35 , GLU D:36BINDING SITE FOR RESIDUE EDO D 117
6AC6SOFTWARELEU E:27 , LYS E:28 , SER E:29 , LEU E:30 , ASP E:31 , HOH E:131BINDING SITE FOR RESIDUE EDO E 119
7AC7SOFTWARESER A:110 , GLU A:111 , PHE A:112 , GLY D:87 , ILE D:88 , THR D:89BINDING SITE FOR RESIDUE EDO A 119
8AC8SOFTWAREGLY A:106 , VAL A:107 , TRP B:56BINDING SITE FOR RESIDUE EDO A 120
9AC9SOFTWAREHIS D:102 , ASN D:103BINDING SITE FOR RESIDUE EDO D 118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OP5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OP5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OP5)

(-) Exons   (0, 0)

(no "Exon" information available for 2OP5)

(-) 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:112
                                                                                                                                                
               SCOP domains d2op5a1 A:4-115 Hypothetical protein GOS_7213774                                                                 SCOP domains
               CATH domains 2op5A01 A:4-108  [code=3.30.70.900, no name defined]                                                     ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 2op5 A   4 TDETAFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNKEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIRS 115
                                    13 |      23        33        43        53        63 |      73        83        93       103       113  
                                      15-MSE                                            65-MSE                                              


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains d2op5b1 B:8-115 Hypothetical protein GOS_7213774                                                            SCOP domains
               CATH domains 2op5B01 B:8-108  [code=3.30.70.900, no name defined]                                                ------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh...eeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 2op5 B   8 AFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIRS 115
                                   |17        27        37        47        57|     | 68        78        88        98       108       
                                  15-MSE                                    57|     |                                                  
                                                                             59     |                                                  
                                                                                   65-MSE                                              


Chain C from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ----d2op5c1 C:4-115 Hypothetical protein GOS_7213774                                                                SCOP domains
               CATH domains 2op5C01 C:0-108  [code=3.30.70.900, no name defined]                                                        ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2op5 C   0 GmKDTDETAFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIRS 115
                             |       9     |  19        29        39        49       |60    |   70        80        90       100       110     
                             1-MSE        15-MSE                                    57|     |                                                  
                                                                                     59     |                                                  
                                                                                           65-MSE                                              


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains d2op5d1 D:8-114 Hypothetical protein GOS_7213774                                                           SCOP domains
               CATH domains 2op5D01 D:8-108  [code=3.30.70.900, no name defined]                                                ------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee.hhhhhhhhhhhhhhh.hhhhhhhhhhhheeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 2op5 D   8 AFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIR 114
                                   |17        27        37        47        57|     | 68        78        88        98       108      
                                  15-MSE                                    57|     |                                                 
                                                                             59     |                                                 
                                                                                   65-MSE                                             


Chain E from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains d2op5e1 E:5-115 Hypothetical protein GOS_7213774                                                                SCOP domains
               CATH domains 2op5E01 E:5-108  [code=3.30.70.900, no name defined]                                                    ------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee......eeeeeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh...eeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 2op5 E   5 DETAFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNKEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIRS 115
                                    14|       24        34        44        54        64|       74        84        94       104       114 
                                     15-MSE                                            65-MSE                                              


Chain F from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains d2op5f1 F:7-114 Hypothetical protein GOS_7213774                                                             SCOP domains
               CATH domains 2op5F01 F:7-108  [code=3.30.70.900, no name defined]                                                  ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhh.hhhhhh...eeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 2op5 F   7 TAFLNSLFmDFTSENELELFLKSLDEVWSEDLYSRLSAAGLIRHVISKVWNKEQHRISmVFEYDSKEGYQKCQEIIDKEFGITLKEKLKKFVFKIHNNRGVVVSEFIR 114
                                    16        26        36        46        56        66        76        86        96       106        
                                   15-MSE                                            65-MSE
   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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OP5)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2OP5)

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