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(-) Description

Title :  ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF THE CYS84ALA CYS85ALA DOUBLE MUTANT OF THE [2FE-2S] FERREDOXIN SUBUNIT OF TOLUENE-4-MONOOXYGENASE FROM PSEUDOMONAS MENDOCINA KR1
 
Authors :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips Jr. , Cent Eukaryotic Structural Genomics (Cesg)
Date :  30 May 07  (Deposition) - 19 Jun 07  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A  (8x)
Biol. Unit 1:  A  (1x)
Keywords :  Ensemble Refinement, Refinement Methodology Development, Ferredoxin, Fes, [2Fe-2S] Cluster, Rieske Protein, Toluene-4-Monooxygenase Subunit, Structural Genomics, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Levin, D. A. Kondrashov, G. E. Wesenberg, G. N. Phillips
Ensemble Refinement Of Protein Crystal Structures: Validation And Application.
Structure V. 15 1040 2007
PubMed-ID: 17850744  |  Reference-DOI: 10.1016/J.STR.2007.06.019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOLUENE-4-MONOOXYGENASE SYSTEM FERREDOXIN SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PT4CD15BTET(C84AC85A)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TMOC
    Mutation: YES
    Organism Scientific: PSEUDOMONAS MENDOCINA
    Organism Taxid: 300
    Strain: KR1
    Synonym: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN C

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit (8x): A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:53 , HOH A:903 , HOH A:904 , HOH A:905 , HOH A:906 , HOH A:907BINDING SITE FOR RESIDUE MG A 901
2AC2SOFTWAREASP A:10 , ASP A:96 , ASP A:97 , HOH A:908 , HOH A:909 , HOH A:910 , HOH A:911BINDING SITE FOR RESIDUE MG A 902
3AC3SOFTWARECYS A:45 , HIS A:47 , CYS A:64 , ALA A:66 , HIS A:67 , LEU A:68 , TRP A:69BINDING SITE FOR RESIDUE FES A 900
4AC4SOFTWARESER A:56 , ARG A:65 , HOH A:1006BINDING SITE FOR RESIDUE EDO A 801
5AC5SOFTWARETRP A:69 , PRO A:81 , ASP A:83BINDING SITE FOR RESIDUE EDO A 802
6AC6SOFTWAREVAL A:14 , ASN A:32 , SER A:33 , GLU A:34 , GLY A:37 , HOH A:1016BINDING SITE FOR RESIDUE EDO A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q3W)

(-) Cis Peptide Bonds  (1, 8)

Asymmetric Unit
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8Asn A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q3W)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.TMOC_PSEME4-100  1A:4-100
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RIESKEPS51296 Rieske [2Fe-2S] iron-sulfur domain profile.TMOC_PSEME4-100  1A:4-100

(-) Exons   (0, 0)

(no "Exon" information available for 2Q3W)

(-) 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:109
 aligned with TMOC_PSEME | Q00458 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:109
                                    11        21        31        41        51        61        71        81        91       101         
           TMOC_PSEME     2 SFEKICSLDDIWVGEMETFETSDGTEVLIVNSEEHGVKAYQAMCPHQEILLSEGSYEGGVITCRAHLWTFNDGTGHGINPDDCCLAEYPVEVKGDDIYVSTKGILPNKA 110
               SCOP domains d2q3wa_ A: Toluene-4-monooxygenase system protein C, TmoC                                                     SCOP domains
               CATH domains 2q3wA00 A:2-110 'Rieske'-like iron-sulphur domains                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh...eeeeee.....eeeeeee...eeeeee........hhhhheee..eee......eee..................eeee..eeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RIESKE  PDB: A:4-100 UniProt: 4-100                                                              ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2q3w A   2 SFEKICSLDDIWVGEMETFETSDGTEVLIVNSEEHGVKAYQAMCPHQEILLSEGSYEGGVITCRAHLWTFNDGTGHGINPDDAALAEYPVEVKGDDIYVSTKGILPNKA 110
                                    11        21        31        41        51        61        71        81        91       101
   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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Q3W)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (TMOC_PSEME | Q00458)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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.
    GO:0042203    toluene catabolic process    The chemical reactions and pathways resulting in the breakdown of toluene, a volatile monoaromatic hydrocarbon found in crude petroleum and petroleum products.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TMOC_PSEME | Q00458: 1sjg 1vm9 4p1b 4p1c

(-) Related Entries Specified in the PDB File

1vm9 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET.