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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE DECAHEME CYTOCHROME MTRF
 
Authors :  T. A. Clarke, M. J. Edwards, D. J. Richardson
Date :  17 Nov 10  (Deposition) - 25 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Greek Key, C Type Cytochrome, Outer Membrane, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Clarke, M. J. Edwards, A. J. Gates, A. Hall, G. F. White, J. Bradley C. L. Reardon, L. Shi, A. S. Beliaev, M. J. Marshall, Z. Wang, N. J. Watmough, J. K. Fredrickson, J. M. Zachara, J. N. Butt, D. J. Richardson
Structure Of A Bacterial Cell Surface Decaheme Electron Conduit.
Proc. Natl. Acad. Sci. Usa V. 108 9384 2011
PubMed-ID: 21606337  |  Reference-DOI: 10.1073/PNAS.1017200108

(-) Compounds

Molecule 1 - DECAHEME CYTOCHROME C MTRF
    Cellular Location: OUTER MEMBRANE
    Chains: A
    Organism Scientific: SHEWANELLA ONEIDENSIS
    Organism Taxid: 211586
    Strain: MR-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2HEC10Ligand/IonHEME C

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:194 , CYS A:197 , HIS A:198 , LYS A:237 , HIS A:238 , THR A:240 , GLY A:241 , PHE A:242 , PRO A:243 , PRO A:540 , HEC A:672 , HEC A:675BINDING SITE FOR RESIDUE HEC A 670
02AC2SOFTWAREPHE A:203 , HIS A:204 , TYR A:208 , ASN A:209 , CYS A:214 , CYS A:217 , HIS A:218 , LYS A:222 , VAL A:223 , SER A:224 , ASN A:225 , ASP A:228 , LYS A:237BINDING SITE FOR RESIDUE HEC A 671
03AC3SOFTWAREARG A:186 , LEU A:188 , VAL A:189 , VAL A:215 , PHE A:230 , PRO A:231 , ILE A:234 , HIS A:235 , HIS A:238 , CYS A:249 , CYS A:252 , HIS A:253 , TRP A:265 , VAL A:268 , HIS A:311 , HEC A:670 , HEC A:673BINDING SITE FOR RESIDUE HEC A 672
04AC4SOFTWAREHIS A:235 , ILE A:246 , SER A:247 , CYS A:274 , CYS A:277 , HIS A:278 , HIS A:311 , HEC A:672 , HEC A:674BINDING SITE FOR RESIDUE HEC A 673
05AC5SOFTWARETHR A:270 , MET A:271 , HIS A:278 , ILE A:281 , PHE A:283 , HIS A:289 , GLN A:292 , ASP A:294 , ASN A:297 , CYS A:298 , CYS A:301 , HIS A:302 , TRP A:306 , VAL A:433 , HEC A:673BINDING SITE FOR RESIDUE HEC A 674
06AC6SOFTWAREPRO A:243 , ILE A:468 , CYS A:473 , CYS A:476 , HIS A:477 , LEU A:482 , ILE A:484 , LEU A:491 , ILE A:523 , HIS A:527 , PHE A:534 , LEU A:537 , TYR A:539 , PRO A:540 , GLN A:548 , CYS A:549 , HEC A:670 , HEC A:677BINDING SITE FOR RESIDUE HEC A 675
07AC7SOFTWARETYR A:369 , ILE A:484 , HIS A:485 , ARG A:488 , ASN A:489 , ASP A:490 , GLN A:494 , CYS A:495 , CYS A:498 , HIS A:499 , LEU A:522BINDING SITE FOR RESIDUE HEC A 676
08AC8SOFTWAREARG A:464 , ARG A:465 , VAL A:467 , ILE A:468 , GLN A:496 , PHE A:519 , LYS A:520 , ILE A:523 , HIS A:524 , HIS A:527 , ILE A:543 , GLY A:544 , CYS A:546 , CYS A:549 , HIS A:550 , THR A:559 , HIS A:636 , HEC A:675 , HEC A:678BINDING SITE FOR RESIDUE HEC A 677
09AC9SOFTWARECYS A:586 , CYS A:589 , HIS A:590 , HIS A:624 , ASP A:631 , VAL A:635 , HIS A:636 , HEC A:677 , HEC A:679BINDING SITE FOR RESIDUE HEC A 678
10BC1SOFTWAREHIS A:590 , THR A:595 , HIS A:598 , ARG A:600 , CYS A:620 , CYS A:623 , HIS A:624 , HEC A:678BINDING SITE FOR RESIDUE HEC A 679
11BC2SOFTWAREASP A:255 , ASN A:256 , LEU A:259 , ARG A:262BINDING SITE FOR RESIDUE CA A 680

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:428 -A:437

(-) Cis Peptide Bonds  (19, 19)

Asymmetric/Biological Unit
No.Residues
1Val A:52 -Asp A:53
2Ile A:57 -Ser A:58
3Tyr A:66 -Gln A:67
4Ser A:81 -Ala A:82
5Phe A:84 -Ile A:85
6Gly A:96 -Ala A:97
7Ala A:133 -Thr A:134
8Leu A:166 -Pro A:167
9Tyr A:208 -Asn A:209
10Glu A:212 -Thr A:213
11Ser A:224 -Asn A:225
12Asn A:225 -Ala A:226
13Ala A:226 -Ala A:227
14Arg A:262 -Gln A:263
15Asp A:479 -Gln A:480
16Ala A:594 -Thr A:595
17Gln A:596 -Asn A:597
18Ala A:613 -Thr A:614
19Thr A:614 -Ala A:615

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PMQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PMQ)

(-) Exons   (0, 0)

(no "Exon" information available for 3PMQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:593
 aligned with Q8EG32_SHEON | Q8EG32 from UniProtKB/TrEMBL  Length:639

    Alignment length:593
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        639  
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638|  
         Q8EG32_SHEON    49 NISVDKVAISDGIAQVDYQVSNQENQAVVGIPSATFIAAQLLPQGATGAGNSSEWQHFTSETCAASCPGTFVDHKNGHYSYRFSATFNGMNGVTFLSDATQRLVIKIGGDALADGTVLPITNQHYDWQSSGNMLAYTRNLVSIDTCNSCHSNLAFHGGRYNQVETCVTCHNSKKVSNAADIFPQMIHSKHLTGFPQSISNCQTCHADNPDLADRQNWYRVPTMEACGACHTQINFPAGQGHPAQTDNSNCVACHNADWTANVHSNAAQTSALAQFNASISSASMDANGTITVAVSLTNPTTGTAYADSADKLKFISDLRIYANWGTSFDYSSRSARSIRLPESTPIAGSNGTYSYNISGLTVPAGTESDRGGLAIQGRVCAKDSVLVDCSTELAEVLVIKSSHSYFNMSALTTTGRREVISNAKCASCHGDQQLNIHGARNDLAGQCQLCHNPNMLADATATNPSMTSFDFKQLIHGLHSSQFAGFEDLNYPGNIGNCAQCHINDSTGISTVALPLNAAVQPLALNNGTFTSPIAAVCSNCHSSDATQNHMRQQGAVFAGTKADATAGTETCAFCHGQGTVADVLKVHPIN--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------Cytochrom_CIII-3pmqA01 A:181-278                                                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................................................................................................eeeee.................eeeee..............hhhhhhhhh.............................hhhhhhhhhh...............................hhhhhhhhh..................hhhhhhhhhhhhhhh.hhhhhhhhh..eeeeeeeee....eeeeeeeee..........hhhhh..eeeeeeeeee.hhhh......eeee.hhh...eee..eeeeeee....hhhhh..eeeeeeeeeeeee..ee........eeee......eee.............hhhhhhh..................hhhhh...................hhhhhhhhhh....................................................hhhhhhhh..............................hhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pmq A  49 NISVDKVAISDGIAQVDYQVSNQENQAVVGIPSATFIAAQLLPQGATGAGNSSEWQHFTSETCAASCPGTFVDHKNGHYSYRFSATFNGMNGVTFLSDATQRLVIKIGGDALADGTVLPITNQHYDWQSSGNMLAYTRNLVSIDTCNSCHSNLAFHGGRYNQVETCVTCHNSKKVSNAADIFPQMIHSKHLTGFPQSISNCQTCHADNPDLADRQNWYRVPTMEACGACHTQINFPAGQGHPAQTDNSNCVACHNADWTANVHSNAAQTSALAQFNASISSASMDANGTITVAVSLTNPTTGTAYADSADKLKFISDLRIYANWGTSFDYSSRSARSIRLPESTPIAGSNGTYSYNISGLTVPAGTESDRGGLAIQGRVCAKDSVLVDCSTELAEVLVIKSSHSYFNMSALTTTGRREVISNAKCASCHGDQQLNIHGARNDLAGQCQLCHNPNMLADATATNPSMTSFDFKQLIHGLHSSQFAGFEDLNYPGNIGNCAQCHINDSTGISTVALPLNAAVQPLALNNGTFTSPIAAVCSNCHSSDATQNHMRQQGAVFAGTKADATAGTETCAFCHGQGTVADVLKVHPINKG 641
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638
   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 3PMQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PMQ)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Multiheme_cytos (34)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8EG32_SHEON | Q8EG32)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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    Ala A:594 - Thr A:595   [ RasMol ]  
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    Arg A:262 - Gln A:263   [ RasMol ]  
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