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(-) Description

Title :  STRUCTURE OF AN ENGINEERED BACTERIAL MICROCOMPARTMENT SHELL PROTEIN BINDING A [4FE-4S] CLUSTER
 
Authors :  M. Sutter, C. Aussignargues, A. Turmo, C. A. Kerfeld
Date :  01 Sep 15  (Deposition) - 03 Feb 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Engineered Protein, Bacterial Microcompartments, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Aussignargues, M. E. Pandelia, M. Sutter, J. S. Plegaria, J. Zarzycki, A. Turmo, J. Huang, D. C. Ducat, E. L. Hegg, B. R. Gibney, C. A. Kerfeld
Structure And Function Of A Bacterial Microcompartment Shel Protein Engineered To Bind A [4Fe-4S] Cluster.
J. Am. Chem. Soc. V. 138 5262 2016
PubMed-ID: 26704697  |  Reference-DOI: 10.1021/JACS.5B11734

(-) Compounds

Molecule 1 - MICROCOMPARTMENTS PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HOCH_5812
    Mutation: YES
    Organism Scientific: HALIANGIUM OCHRACEUM (STRAIN DSM 14365 / JCM 11303 / SMP-2)
    Organism Taxid: 502025
    Strain: DSM 14365 / JCM 11303 / SMP-2

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:55 , ALA A:157 , CYS B:55 , ALA B:157 , HOH B:381 , CYS C:55 , ALA C:157binding site for residue SF4 A 301
2AC2SOFTWARECYS D:55 , ALA D:157 , CYS E:55 , ALA E:157 , CYS F:55 , ALA F:157 , HOH F:368binding site for residue SF4 D 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DII)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DII)

(-) 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:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee......hhhhh.........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii A   5 PERFDATPPEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDELRGRLFF 205
                                    16        26        36        46        56        66        76        86        96       106      |121       131       141       151       161       171       181       191       201    
                                   13|                                                                                              113|                                                                                      
                                    16                                                                                               119                                                                                      


Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee......hhhhh..........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii B   6 ERFDATPPAGEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDELRGRLFF 205
                                    15        25        35        45        55        65        75        85        95       105       119       129       139       149       159       169       179       189       199      
                                                                                                                                      114|                                                                                      
                                                                                                                                       119                                                                                      


Chain C from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh..........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii C   1 MDHAPERFDATPPEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDELRGRLFF 205
                                    10  ||    22        32        42        52        62        72        82        92       102       112 ||    126       136       146       156       166       176       186       196         
                                       13|                                                                                               114|                                                                                      
                                        16                                                                                                119                                                                                      


Chain D from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee......hhhhh..............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii D   4 APERFDATPPAGEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWEEDTESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDGRLFF 205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193   ||    
                                                                                                                                                                                                                           197|    
                                                                                                                                                                                                                            201    


Chain E from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee......hhhhh..........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii E   7 RFDATPPAGEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDELRGRLFF 205
                                    16        26        36        46        56        66        76        86        96       106       120       130       140       150       160       170       180       190       200     
                                                                                                                                     114|                                                                                      
                                                                                                                                      119                                                                                      


Chain F from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeeee...eeeeeeeehhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhh..........eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee.......eeeeeeehhhhhhhhhhhhhhhhh..eeeeeee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dii F   5 PERFDATPPAGEPDRPALGVLELTSIARGITVADAALKRAPSLLLMSRPVCSGKHLLMMRGQVAEVEESMIAAREIAGAGSGALLDELELPYAHEQLWRFLDAPVVADAWESVIIVETATVCAAIDSADAALKTAPVVLRDMRLAIGIAGKAFFTLTGELADVEAAAEVVRERCGARLLELACIARPVDELRGRLFF 205
                                    14        24        34        44        54        64        74        84        94       104       114|      128       138       148       158       168       178       188       198       
                                                                                                                                       114|                                                                                      
                                                                                                                                        119
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  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 5DII)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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(-) Related Entries Specified in the PDB File

5dih 5djb