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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OUTER MEMBRANE DECAHEME CYTOCHROME MTRC
 
Authors :  T. A. Clarke, M. J. Edwards
Date :  10 Jul 13  (Deposition) - 11 Feb 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Greek Key, C Type Cytochrome Electron Transport, Outer Membrane, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Edwards, G. F. White, M. Norman, A. Tome-Fernandez, E. Ainsworth L. Shi, J. K. Fredrickson, J. M. Zachara, J. N. Butt, D. J. Richardson, T. A. Clarke
Redox Linked Flavin Sites In Extracellular Decaheme Protein Involved In Microbe-Mineral Electron Transfer.
Sci Rep V. 5 11677 2015
PubMed-ID: 26126857  |  Reference-DOI: 10.1038/SREP11677

(-) Compounds

Molecule 1 - EXTRACELLULAR IRON OXIDE RESPIRATORY SYSTEM SURFACE DECAHEME CYTOCHROME C COMPONENT MTRC
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MTRC (UNP RESIDUES 26-671)
    Gene: MTRC, SO_1778
    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  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CA5Ligand/IonCALCIUM ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4HEC10Ligand/IonHEME C

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:185 , CYS A:186 , CYS A:189 , HIS A:190 , ILE A:196 , ILE A:229 , VAL A:232 , HIS A:233 , TRP A:239 , LYS A:244 , ALA A:249 , GLY A:570 , HEC A:802 , HOH A:961 , HOH A:983 , HOH A:1170 , HOH A:1562BINDING SITE FOR RESIDUE HEC A 801
02AC2SOFTWARELYS A:86 , ILE A:196 , TYR A:197 , HIS A:198 , GLN A:199 , ALA A:200 , THR A:205 , CYS A:206 , CYS A:209 , HIS A:210 , PHE A:214 , ARG A:218 , LYS A:220 , HIS A:222 , LEU A:228 , TRP A:239 , GLY A:240 , GLU A:630 , HEC A:801 , HOH A:1005 , HOH A:1035 , HOH A:1441 , HOH A:1809BINDING SITE FOR RESIDUE HEC A 802
03AC3SOFTWARESER A:102 , ILE A:180 , VAL A:181 , SER A:226 , ILE A:229 , HIS A:230 , HIS A:233 , VAL A:253 , ASP A:255 , CYS A:257 , CYS A:260 , HIS A:261 , ASN A:272 , TRP A:273 , ILE A:276 , VAL A:281 , HIS A:319 , HEC A:804 , HOH A:905 , HOH A:929 , HOH A:953 , HOH A:981 , HOH A:1077 , HOH A:1797BINDING SITE FOR RESIDUE HEC A 803
04AC4SOFTWAREASP A:255 , CYS A:282 , SER A:284 , CYS A:285 , HIS A:286 , LEU A:318 , HIS A:319 , LYS A:322 , HEC A:803 , HEC A:805 , HOH A:1357BINDING SITE FOR RESIDUE HEC A 804
05AC5SOFTWARETHR A:278 , MET A:279 , HIS A:286 , ILE A:289 , PHE A:291 , HIS A:297 , GLN A:300 , ASP A:302 , ASN A:305 , CYS A:306 , CYS A:309 , HIS A:310 , HEC A:804 , HOH A:1097 , HOH A:1573BINDING SITE FOR RESIDUE HEC A 805
06AC6SOFTWARECYS A:189 , ASN A:251 , ALA A:495 , CYS A:496 , CYS A:499 , HIS A:500 , PHE A:504 , LEU A:535 , LEU A:560 , LYS A:563 , HIS A:564 , ALA A:568 , LEU A:571 , ILE A:572 , SER A:578 , HEC A:807 , HOH A:1174 , HOH A:1364 , HOH A:1421 , HOH A:1473BINDING SITE FOR RESIDUE HEC A 806
07AC7SOFTWARETYR A:389 , PHE A:438 , HIS A:507 , HIS A:512 , CYS A:538 , THR A:540 , CYS A:541 , HIS A:542 , THR A:547 , TYR A:548 , ASN A:552 , LYS A:559 , LYS A:563 , HEC A:806 , HOH A:914 , HOH A:1343 , HOH A:1488 , HOH A:1561BINDING SITE FOR RESIDUE HEC A 807
08AC8SOFTWAREARG A:486 , HIS A:487 , SER A:490 , LEU A:535 , GLU A:557 , LEU A:560 , HIS A:561 , HIS A:564 , CYS A:576 , CYS A:579 , HIS A:580 , PHE A:583 , ASN A:584 , HIS A:666 , HEC A:809 , HOH A:902 , HOH A:909BINDING SITE FOR RESIDUE HEC A 808
09AC9SOFTWAREHIS A:561 , LYS A:589 , THR A:613 , CYS A:614 , CYS A:617 , HIS A:618 , HIS A:659 , HIS A:666 , THR A:667 , HEC A:808 , HEC A:810 , EDO A:821 , HOH A:1204 , HOH A:1820BINDING SITE FOR RESIDUE HEC A 809
10BC1SOFTWARETHR A:611 , HIS A:618 , TYR A:624 , MET A:625 , VAL A:626 , HIS A:627 , PHE A:635 , CYS A:655 , CYS A:658 , HIS A:659 , HEC A:809 , HOH A:936 , HOH A:988 , HOH A:1103 , HOH A:1820BINDING SITE FOR RESIDUE HEC A 810
11BC2SOFTWAREASP A:52 , ILE A:53 , GLU A:165 , HOH A:939 , HOH A:970 , HOH A:1451BINDING SITE FOR RESIDUE CA A 811
12BC3SOFTWAREASN A:231 , ASN A:234 , LYS A:237 , HOH A:1032BINDING SITE FOR RESIDUE CA A 812
13BC4SOFTWAREASP A:472 , GLN A:520 , HOH A:965 , HOH A:995 , HOH A:1063 , HOH A:1087 , HOH A:1490BINDING SITE FOR RESIDUE CA A 813
14BC5SOFTWAREGLN A:651 , HOH A:1282 , HOH A:1323 , HOH A:1836BINDING SITE FOR RESIDUE CA A 814
15BC6SOFTWAREGLU A:162 , GLU A:202 , HOH A:1040 , HOH A:1410 , HOH A:1452 , HOH A:1453BINDING SITE FOR RESIDUE CA A 815
16BC7SOFTWAREGLY A:570 , THR A:654 , HOH A:1229BINDING SITE FOR RESIDUE EDO A 816
17BC8SOFTWAREASP A:52 , THR A:54 , PHE A:68 , ASN A:136 , HOH A:996 , HOH A:1404BINDING SITE FOR RESIDUE EDO A 817
18BC9SOFTWAREGLY A:574 , CYS A:576 , VAL A:663 , ALA A:664 , ASP A:665 , HIS A:666 , HOH A:1505BINDING SITE FOR RESIDUE EDO A 818
19CC1SOFTWAREGLU A:586 , GLN A:623 , PHE A:656 , HOH A:1107 , HOH A:1126 , HOH A:1319BINDING SITE FOR RESIDUE EDO A 819
20CC2SOFTWARESER A:304 , ASN A:305 , ALA A:457 , HOH A:1647BINDING SITE FOR RESIDUE EDO A 820
21CC3SOFTWAREHIS A:564 , VAL A:565 , TYR A:569 , ILE A:572 , GLY A:573 , HEC A:809BINDING SITE FOR RESIDUE EDO A 821
22CC4SOFTWARETHR A:326 , VAL A:463 , GLU A:505 , LYS A:508 , HOH A:1098 , HOH A:1366BINDING SITE FOR RESIDUE EDO A 822
23CC5SOFTWAREASN A:331 , LYS A:470 , GLU A:503 , HOH A:1362BINDING SITE FOR RESIDUE EDO A 823
24CC6SOFTWAREMET A:493 , THR A:494 , ALA A:497 , ALA A:502 , VAL A:533 , HOH A:1269 , HOH A:1303BINDING SITE FOR RESIDUE ACT A 824

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:444 -A:453

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LM8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LM8)

(-) Exons   (0, 0)

(no "Exon" information available for 4LM8)

(-) 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:626
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee......eeeeeee............eeeeeeeeee...........eeeeeeee..eee....eeee................eeeeeee..ee.....ee..eeeeeee..............hhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh.hhhhh..........hhhhhh.hhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......eeeeeeee.....eehhhhhhh.eeeeeeeeee............eeeeeee..ee...eee.....eeee..........hhhh.eeeeeeeeeeeee..ee...........hhh.eee...eeeeee..............hhhhhhhhhh................hhhhh............hhhhhhh.............hhhhhhhhhhhhhhhhhhh.hhhhh....hhhhhhhh..eeeee.....eeeehhhhhhhhh...........hhhhhhhh......hhhhhhhh....hhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lm8 A  45 SIQTLNLDITKVSYENGAPMVTVFATNEADMPVIGLANLEIKKALQLIPEGATGPGNSANWQGLGSSKSYVDNKNGSYTFKFDAFDSNKVFNAQLTQRFNVVSAAGKLADGTTVPVAEMVEDFDGQGNAPQYTKNIVSHEVCASCHVEGEKIYHQATEVETCISCHTQEFADGRGKPHVAFSHLIHNVHNANKAWGKDNKIPTVAQNIVQDNCQVCHVESDMLTEAKNWSRIPTMEVCSSCHVDIDFAAGKGHSQQLDNSNCIACHNSDWTAELHTAKTTATKNLINQYGIETTSTINTETKAATISVQVVDANGTAVDLKTILPKVQRLEIITNVGPNNATLGYSGKDSIFAIKNGALDPKATINDAGKLVYTTTKDLKLGQNGADSDTAFSFVGWSMCSSEGKFVDCADPAFDGVDVTKYTGMKADLAFATLSGKAPSTRHVDSVNMTACANCHTAEFEIHKGKQHAGFVMTEQLSHTQDANGKAIVGLDACVTCHTPDGTYSFANRGALELKLHKKHVEDAYGLIGGNCASCHSDFNLESFKKKGALNTAAAADKTGLYSTPITATCTTCHTVGSQYMVHTKETLESFGAVVDGTKDDATSAAQSETCFYCHTPTVADHTKVK 670
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664
   Legend:   → Mismatch (orange background)
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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 4LM8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LM8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LM8)

(-) Gene Ontology  (2, 2)

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(-) Related Entries Specified in the PDB File

3pmq CRYSTAL STRUCTURE OF THE OUTER MEMBRANE DECAHEME CYTOCHROME MTRF
3ucp OUTER MEMBRANE ENDECAHEME CYTOCHROME UNDA FROM SHEWANELLA SP. HRCR-6
4lmh