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(-) Description

Title :  CRYSTAL STRUCTURE OF UNDA COMPLEXED WITH IRON NITRILOTRIACETATE
 
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 :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  C-Type Cytochrome, Electron Transport, Outer Membrane, 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, 28)

Asymmetric/Biological Unit (7, 28)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FE4Ligand/IonFE (III) ION
3GOL4Ligand/IonGLYCEROL
4HEC11Ligand/IonHEME C
5MG2Ligand/IonMAGNESIUM ION
6NTA4Ligand/IonNITRILOTRIACETIC ACID
7O2Ligand/IonOXYGEN ATOM

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:251 , CYS A:252 , CYS A:255 , HIS A:256 , HIS A:310 , THR A:353 , VAL A:356 , SER A:363 , CYS A:364 , THR A:743 , PRO A:745 , HOH A:1068 , HOH A:1538 , HOH A:1680BINDING SITE FOR RESIDUE HEC A 901
02AC2SOFTWAREGLN A:158 , ASN A:160 , ILE A:161 , 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:305 , MET A:316 , VAL A:317 , GLY A:318 , CA A:912 , HOH A:1488 , HOH A:1511 , HOH A:1535BINDING SITE FOR RESIDUE HEC A 902
03AC3SOFTWARETHR A:110 , GLN A:112 , ARG A:243 , GLN A:284 , MET A:302 , GLY A:303 , VAL A:306 , HIS A:307 , HIS A:310 , 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:904 , HOH A:1331 , HOH A:1468 , HOH A:1577BINDING SITE FOR RESIDUE HEC A 903
04AC4SOFTWAREHIS A:307 , ILE A:358 , GLY A:359 , ALA A:385 , CYS A:386 , CYS A:389 , HIS A:390 , ASN A:434 , LEU A:435 , SER A:456 , TYR A:459 , HIS A:460 , LYS A:463 , HEC A:903 , HOH A:1002 , HOH A:1525 , HOH A:1620 , HOH A:1639 , HOH A:1778 , HOH A:1910BINDING SITE FOR RESIDUE HEC A 904
05AC5SOFTWAREGLY 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 , PHE A:439 , CYS A:444 , CYS A:447 , HIS A:448 , HOH A:1405 , HOH A:1531 , HOH A:1665 , HOH A:1845BINDING SITE FOR RESIDUE HEC A 905
06AC6SOFTWARETHR A:353 , ILE A:648 , LYS A:652 , CYS A:653 , CYS A:656 , HIS A:657 , PHE A:663 , SER A:666 , ILE A:724 , HIS A:728 , ARG A:735 , ALA A:742 , THR A:743 , PHE A:744 , GLU A:746 , ALA A:753 , HEC A:908 , HOH A:1228 , HOH A:1248 , HOH A:1259 , HOH A:1294 , HOH A:1309 , HOH A:1632 , HOH A:1825BINDING SITE FOR RESIDUE HEC A 906
07AC7SOFTWAREMET A:525 , ARG A:528 , ARG A:536 , THR A:670 , HIS A:671 , CYS A:680 , CYS A:683 , HIS A:684 , PRO A:707 , HIS A:709 , SER A:710 , LYS A:711 , LYS A:712 , PHE A:718 , ARG A:736 , HEC A:908 , NTA A:919 , HOH A:1003 , HOH A:1218BINDING SITE FOR RESIDUE HEC A 907
08AC8SOFTWAREPHE A:663 , 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 , ARG A:732 , ARG A:735 , ARG A:736 , HEC A:906 , HEC A:907 , MG A:913 , HOH A:1004 , HOH A:1224 , HOH A:1228BINDING SITE FOR RESIDUE HEC A 908
09AC9SOFTWAREARG 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 , ALA A:749 , CYS A:751 , CYS A:754 , HIS A:755 , LEU A:762 , ALA A:784 , VAL A:835 , HIS A:839 , HEC A:910 , HOH A:1274 , HOH A:1297 , HOH A:1308 , HOH A:1333 , HOH A:1455 , HOH A:1964BINDING SITE FOR RESIDUE HEC A 909
10BC1SOFTWARESER 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:909 , HEC A:911 , HOH A:1114BINDING SITE FOR RESIDUE HEC A 910
11BC2SOFTWAREHIS 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:910 , HOH A:1114 , HOH A:1737BINDING SITE FOR RESIDUE HEC A 911
12BC3SOFTWAREASP A:293 , GLU A:295 , VAL A:317 , HEC A:902 , HOH A:1488 , HOH A:1535BINDING SITE FOR RESIDUE CA A 912
13BC4SOFTWAREHIS A:667 , THR A:670 , HIS A:684 , HEC A:908BINDING SITE FOR RESIDUE MG A 913
14BC5SOFTWAREVAL A:548 , ASN A:551 , LEU A:554 , HOH A:1390 , HOH A:1472 , HOH A:1537BINDING SITE FOR RESIDUE MG A 914
15BC6SOFTWAREFE A:916 , O A:917 , NTA A:918 , HOH A:1009BINDING SITE FOR RESIDUE FE A 915
16BC7SOFTWAREFE A:915 , O A:917 , NTA A:919 , HOH A:1193BINDING SITE FOR RESIDUE FE A 916
17BC8SOFTWAREARG A:528 , HIS A:709 , SER A:710 , FE A:915 , FE A:916 , NTA A:918 , NTA A:919BINDING SITE FOR RESIDUE O A 917
18BC9SOFTWAREHIS A:709 , SER A:710 , LYS A:711 , FE A:915 , O A:917 , NTA A:919 , HOH A:1009 , HOH A:1351BINDING SITE FOR RESIDUE NTA A 918
19CC1SOFTWAREARG A:528 , HIS A:709 , SER A:710 , HEC A:907 , FE A:916 , O A:917 , NTA A:918 , HOH A:1181 , HOH A:1193BINDING SITE FOR RESIDUE NTA A 919
20CC2SOFTWAREGLU A:659 , FE A:921 , O A:922 , NTA A:924BINDING SITE FOR RESIDUE FE A 920
21CC3SOFTWAREGLU A:659 , FE A:920 , O A:922 , NTA A:923BINDING SITE FOR RESIDUE FE A 921
22CC4SOFTWAREGLU A:659 , FE A:920 , FE A:921 , NTA A:923 , NTA A:924BINDING SITE FOR RESIDUE O A 922
23CC5SOFTWARELYS A:468 , ARG A:471 , GLU A:659 , LYS A:660 , FE A:921 , O A:922 , HOH A:1196BINDING SITE FOR RESIDUE NTA A 923
24CC6SOFTWAREGLU A:659 , LYS A:660 , FE A:920 , O A:922 , HOH A:1010 , HOH A:1195 , HOH A:1445BINDING SITE FOR RESIDUE NTA A 924
25CC7SOFTWARETYR A:421 , TYR A:422 , ALA A:423 , THR A:424 , HOH A:1601 , HOH A:1791BINDING SITE FOR RESIDUE GOL A 925
26CC8SOFTWAREASN A:160 , ARG A:277 , HOH A:1511 , HOH A:1753BINDING SITE FOR RESIDUE GOL A 926
27CC9SOFTWAREGLN A:362 , HIS A:365 , SER A:366 , THR A:367 , ASP A:368 , HOH A:1265 , HOH A:1359BINDING SITE FOR RESIDUE GOL A 927
28DC1SOFTWAREASP A:730 , SER A:733 , VAL A:734 , ARG A:735 , THR A:738 , THR A:739 , ASP A:740 , ALA A:741 , HOH A:1602BINDING SITE FOR RESIDUE GOL A 928

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:687 -Pro A:688

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UFK)

(-) 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 .ee.......eeeeeeeeee..eeeeeeeee......eehhhhh..eeeeeeeeeeee..........eeee..eeee..hhhhh...eeeeeee.....eeeeee......eeee.....hhhh.eeeee..eeeeeeeee.hhh...............eeeeeeeee.......eeeeeeeehhhhh....hhhhh....hhhhhh...................hhhhh..hhhhhhhhh.............hhhhhhhhhhh...eee.hhh.eee..hhhhhhhhhhh.........ee..........hhhhh.........hhhhhhh.hhhhhhhhhh.......hhhhhh.......hhhhhhhhhh............hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..ee..eeee....eeeeeee.....hhhhh..eeeeeeeeee......................eeeee.hhh.....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
                 3ufk 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 3UFK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        F8UWD6_9GAMM | F8UWD6: 3ucp 3ufh

(-) Related Entries Specified in the PDB File

3ucp RECOMBINANT SOLUBLE UNDA
3ufh RECOMBINANT SOLUBLE UNDA COMPLEXED WITH IRON CITRATE