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(-) Description

Title :  CRYSTAL STRUCTURE OF UNDA WITH IRON CITRATE BOUND
 
Authors :  M. J. Edwards, T. A. Clarke
Date :  01 Nov 11  (Deposition) - 08 Aug 12  (Release) - 08 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A
Keywords :  C-Type Cytochrome, Electron Transfer, C-Type Hemes, Outermembrane, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Edwards, A. Hall, L. Shi, J. K. Fredrickson, J. M. Zachara, J. N. Butt, D. J. Richardson, T. A. Clarke
The Crystal Structure Of The Extracellular 11-Heme Cytochrome Unda Reveals A Conserved 10-Heme Motif And Defined Binding Site For Soluble Iron Chelates.
Structure V. 20 1275 2012
PubMed-ID: 22682743  |  Reference-DOI: 10.1016/J.STR.2012.04.016

(-) Compounds

Molecule 1 - UNDA
    Chains: A
    Engineered: YES
    Expression System: SHEWANELLA ONEIDENSIS
    Expression System Plasmid: PBAD
    Expression System Strain: MR-1
    Expression System Taxid: 70863
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE DOMAIN
    Gene: UNDA
    Organism Scientific: SHEWANELLA SP. HRCR_06
    Organism Taxid: 1043181

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric/Biological Unit (7, 22)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FE3Ligand/IonFE (III) ION
3FLC3Ligand/IonCITRATE ANION
4GOL1Ligand/IonGLYCEROL
5HEC11Ligand/IonHEME C
6MG2Ligand/IonMAGNESIUM ION
7O1Ligand/IonOXYGEN ATOM

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:789 , HIS A:801 , PHE A:802 , ASN A:805 , THR A:822 , CYS A:823 , CYS A:826 , HIS A:827 , PHE A:833 , HEC A:911 , HOH A:1797BINDING SITE FOR RESIDUE HEC A 901
02AC2SOFTWAREARG A:644 , VAL A:647 , ILE A:648 , PHE A:720 , LYS A:721 , ILE A:724 , HIS A:725 , HIS A:728 , PRO A:748 , CYS A:751 , CYS A:754 , HIS A:755 , LEU A:760 , LEU A:762 , HIS A:839 , HEC A:911 , HOH A:1119 , HOH A:1205 , HOH A:1229 , HOH A:1304 , HOH A:1649BINDING SITE FOR RESIDUE HEC A 902
03AC3SOFTWARETHR A:353 , ILE A:648 , LYS A:652 , CYS A:653 , CYS A:656 , HIS A:657 , SER A:666 , ILE A:724 , HIS A:728 , ARG A:735 , THR A:743 , PHE A:744 , ALA A:753 , HEC A:905 , GOL A:922 , HOH A:1082 , HOH A:1093 , HOH A:1094 , HOH A:1131 , HOH A:1331 , HOH A:1492 , HOH A:1605BINDING SITE FOR RESIDUE HEC A 903
04AC4SOFTWAREMET A:525 , ARG A:528 , ARG A:536 , THR A:670 , HIS A:671 , CYS A:680 , CYS A:683 , HIS A:684 , HIS A:709 , SER A:710 , LYS A:711 , LYS A:712 , PHE A:718 , ARG A:736 , HEC A:905 , FLC A:919 , HOH A:1024 , HOH A:1028BINDING SITE FOR RESIDUE HEC A 904
05AC5SOFTWAREARG A:540 , HIS A:667 , LEU A:669 , THR A:670 , THR A:682 , CYS A:683 , HIS A:684 , ASN A:689 , CYS A:699 , CYS A:702 , HIS A:703 , PHE A:718 , MET A:723 , ARG A:732 , ARG A:735 , ARG A:736 , HEC A:903 , HEC A:904 , MG A:914 , HOH A:1034 , HOH A:1045 , HOH A:1093BINDING SITE FOR RESIDUE HEC A 905
06AC6SOFTWAREASN A:251 , CYS A:252 , CYS A:255 , HIS A:256 , LEU A:272 , HIS A:310 , VAL A:356 , SER A:363 , CYS A:656 , THR A:743 , PRO A:745 , HOH A:1511 , HOH A:1586 , HOH A:1652 , HOH A:1722BINDING SITE FOR RESIDUE HEC A 906
07AC7SOFTWAREGLN A:158 , ASN A:160 , LEU A:272 , HIS A:273 , ARG A:277 , ILE A:278 , ASN A:282 , CYS A:283 , CYS A:286 , HIS A:287 , ASP A:293 , MET A:316 , VAL A:317 , GLY A:318 , CA A:913 , HOH A:1168 , HOH A:1412 , HOH A:1639 , HOH A:1673BINDING SITE FOR RESIDUE HEC A 907
08AC8SOFTWARETHR A:110 , GLN A:112 , ARG A:243 , GLN A:284 , MET A:302 , GLY A:303 , HIS A:307 , HIS A:310 , GLY A:359 , CYS A:361 , CYS A:364 , HIS A:365 , SER A:377 , PHE A:378 , HIS A:380 , LYS A:382 , ALA A:385 , HIS A:460 , HEC A:909 , HOH A:1414 , HOH A:1646BINDING SITE FOR RESIDUE HEC A 908
09AC9SOFTWAREHIS A:307 , ILE A:358 , GLY A:359 , HIS A:380 , ALA A:385 , CYS A:386 , CYS A:389 , HIS A:390 , VAL A:433 , ASN A:434 , LEU A:435 , SER A:456 , TYR A:459 , HIS A:460 , LYS A:463 , HEC A:908 , HOH A:1001 , HOH A:1392 , HOH A:1469 , HOH A:1651 , HOH A:1707BINDING SITE FOR RESIDUE HEC A 909
10BC1SOFTWAREGLY A:105 , LYS A:106 , LYS A:109 , HIS A:381 , GLY A:383 , ARG A:412 , GLY A:416 , PHE A:419 , HIS A:420 , LEU A:435 , PHE A:439 , CYS A:444 , CYS A:447 , HIS A:448 , HOH A:1216 , HOH A:1467 , HOH A:1640 , HOH A:1696BINDING SITE FOR RESIDUE HEC A 910
11BC2SOFTWARESER A:264 , SER A:265 , THR A:266 , GLU A:407 , HIS A:725 , PRO A:748 , ALA A:784 , CYS A:785 , CYS A:788 , HIS A:789 , HIS A:827 , VAL A:835 , VAL A:838 , HIS A:839 , HEC A:901 , HEC A:902BINDING SITE FOR RESIDUE HEC A 911
12BC3SOFTWAREVAL A:548 , ASN A:551 , LEU A:554 , HOH A:1199 , HOH A:1265 , HOH A:1271BINDING SITE FOR RESIDUE MG A 912
13BC4SOFTWAREASP A:293 , GLU A:295 , VAL A:317 , HEC A:907 , HOH A:1168 , HOH A:1412BINDING SITE FOR RESIDUE CA A 913
14BC5SOFTWAREHIS A:667 , THR A:670 , HIS A:684 , HEC A:905BINDING SITE FOR RESIDUE MG A 914
15BC6SOFTWAREFE A:916 , FE A:917 , FLC A:919 , FLC A:920 , O A:921 , HOH A:1018BINDING SITE FOR RESIDUE FE A 915
16BC7SOFTWAREFE A:915 , FE A:917 , FLC A:918 , FLC A:919 , O A:921BINDING SITE FOR RESIDUE FE A 916
17BC8SOFTWAREFE A:915 , FE A:916 , FLC A:918 , FLC A:919 , FLC A:920BINDING SITE FOR RESIDUE FE A 917
18BC9SOFTWARETHR A:491 , PHE A:492 , THR A:493 , THR A:564 , FE A:916 , FE A:917 , FLC A:919 , FLC A:920 , O A:921 , HOH A:1002 , HOH A:1033 , HOH A:1129BINDING SITE FOR RESIDUE FLC A 918
19CC1SOFTWAREARG A:528 , HIS A:709 , SER A:710 , HEC A:904 , FE A:915 , FE A:916 , FE A:917 , FLC A:918 , FLC A:920 , O A:921 , HOH A:1018 , HOH A:1060BINDING SITE FOR RESIDUE FLC A 919
20CC2SOFTWAREFE A:915 , FE A:917 , FLC A:918 , FLC A:919 , O A:921 , HOH A:1002 , HOH A:1003 , HOH A:1315BINDING SITE FOR RESIDUE FLC A 920
21CC3SOFTWAREFE A:915 , FE A:916 , FLC A:918 , FLC A:919 , FLC A:920 , HOH A:1017 , HOH A:1018 , HOH A:1315BINDING SITE FOR RESIDUE O A 921
22CC4SOFTWAREPRO A:355 , HIS A:657 , ASP A:662 , PHE A:663 , HEC A:903 , HOH A:1331BINDING SITE FOR RESIDUE GOL A 922

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:165 -A:169
2A:599 -A:615

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:44 -Leu A:45
2Val A:687 -Pro A:688

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UFH)

(-) 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:800
 aligned with F8UWD6_9GAMM | F8UWD6 from UniProtKB/TrEMBL  Length:843

    Alignment length:800
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843
         F8UWD6_9GAMM    44 GLDISQATTLKATLEDVKIDNGTVSVDIVLTNANGVPVTGLEQYAQINAIGLGIAKLTPESGKGYKTPQWVSYINSVKAADPARSLANYSYTDGKDSAGNPITKEVKFTPGDAIQANIESSCKTTCLTVVDSGVYRYTFQTNLSTLPAIEGLDLTYDPTLIHRITLELQTDGSKDAKLVNSHIDFLPSDNFRVAKETETRTVVDLEANCIKCHSTNYSDTSSTAKPLALHGGRRIGIANCQVCHTSYSKDPETGSPLDMGAMVHAIHKGTYAMVGYSGTAYDFSGTMAKAAAESGYPQYREGKDVSERVTLPVSIGNCQSCHSTDDKGPVDAASFKHHKGLACASCHMSGFNPVDNSEWLTPPEGQKDRGFVGNYFHYYATPEIDGIPGVNLVHVFQNGGCASCHAEQGEEGSAKYHLAKANATKLLRTEYAYKLENGTFDVAKGELTFTVNWHSDVAPHQDPKVKEFWVSLTAFNGTEYTMGPRPSNGTLGRSENRISVNLAKVETNANLTAVPNGSKVTYTLTGIKAVIGTSSVPYKQIVSIGKGFMDGKLLICANSAELDPTMDAAIDCSNTEAPIYEVIVGSNKASFSADASNVTARSIVISEAKCANCHGEKADFSASHALTHAADKPDNSCGTCHSAVPNTAVALADGSCVACHNGAPAHSKKPFERGFDFKVMIHQIHADTRSVRRLTTDAATFPENPANCAACHDKGQLSLATLGNKPAFLASTGEYSPTVAACASCHATTATDSAVIGHFETNGGVYNAAAGTYTPGSETCATCHGEGKSFGVDKVHPVKY 843
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee......eeeeeeeee........hhhhh..eeeeeeeeeeee..........eeee..eeee..hhhhh...eeeeeee.....eeeeee......eeee.....hhhhhh......eeeeeeeee...................eeeeeeeee.......eeeeeeeee.....ee..........hhhhhh..........................hhhhhhhhh.............hhhhhhhhhhh...eee.hhh.eee..hhhhhhhhhhh.........ee..........hhhhh.........hhhhhhh.hhhhhhhhhh.......hhhhhh.......hhhhhhhhhh............hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..ee..eeee....eeeeeee.....hhhhh..eeeeeeeeee......................eeeee.hhhhhh..eeeeee..eeeeee.............hhhhhhhh.eeeeeeeeeeee....................eeeeee....eeee.............hhhhhhhhhh....hhhhhh...........hhhhhh...........................hhhhh.hhhhhhhhhhh....................hhhhh.........hhhhh..ee....eehhhhhhhhhhhh....hhhhhhhhhhh.................hhhhhh.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ufh A  44 GLDISQATTLKATLEDVKIDNGTVSVDIVLTNANGVPVTGLEQYAQINAIGLGIAKLTPESGKGYKTPQWVSYINSVKAADPARSLANYSYTDGKDSAGNPITKEVKFTPGDAIQANIESSCKTTCLTVVDSGVYRYTFQTNLSTLPAIEGLDLTYDPTLIHRITLELQTDGSKDAKLVNSHIDFLPSDNFRVAKETETRTVVDLEANCIKCHSTNYSDTSSTAKPLALHGGRRIGIANCQVCHTSYSKDPETGSPLDMGAMVHAIHKGTYAMVGYSGTAYDFSGTMAKAAAESGYPQYREGKDVSERVTLPVSIGNCQSCHSTDDKGPVDAASFKHHKGLACASCHMSGFNPVDNSEWLTPPEGQKDRGFVGNYFHYYATPEIDGIPGVNLVHVFQNGGCASCHAEQGEEGSAKYHLAKANATKLLRTEYAYKLENGTFDVAKGELTFTVNWHSDVAPHQDPKVKEFWVSLTAFNGTEYTMGPRPSNGTLGRSENRISVNLAKVETNANLTAVPNGSKVTYTLTGIKAVIGTSSVPYKQIVSIGKGFMDGKLLICANSAELDPTMDAAIDCSNTEAPIYEVIVGSNKASFSADASNVTARSIVISEAKCANCHGEKADFSASHALTHAADKPDNSCGTCHSAVPNTAVALADGSCVACHNGAPAHSKKPFERGFDFKVMIHQIHADTRSVRRLTTDAATFPENPANCAACHDKGQLSLATLGNKPAFLASTGEYSPTVAACASCHATTATDSAVIGHFETNGGVYNAAAGTYTPGSETCATCHGEGKSFGVDKVHPVKY 843
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       833       843
   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 3UFH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UFH)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (F8UWD6_9GAMM | F8UWD6)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/TrEMBL
        F8UWD6_9GAMM | F8UWD6: 3ucp 3ufk

(-) Related Entries Specified in the PDB File

3ucp RECOMBINANT SOLUBLE FORM OF UNDA
3ufk