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(-) Description

Title :  THIOL-DISULFIDE OXIDOREDUCTASE FROM BACTEROIDES FRAGILIS NCTC 9343
 
Authors :  N. E. C. Duke, L. Freeman, C. Tesar, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  16 Dec 08  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thiol Disulfide Oxidoreductase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. E. C. Duke, L. Freeman, C. Tesar, A. Joachimiak
Thiol-Disulfide Oxidoreductase From Bacteroides Fragilis Nctc 9343
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THIOL-DISULFIDE OXIDOREDUCTASE
    Chains: A, B, C, D
    EC Number: 1.8.4.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 203-347
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Strain: NCTC 9343

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:19 , GLU A:26 , ARG A:27 , HOH A:411BINDING SITE FOR RESIDUE ACT A 501
2AC2SOFTWAREGLU B:19 , GLU B:26 , ARG B:27 , HOH B:412BINDING SITE FOR RESIDUE ACT B 502
3AC3SOFTWAREALA C:25 , GLU C:26 , ARG C:27 , HOH C:413BINDING SITE FOR RESIDUE ACT C 503
4AC4SOFTWAREGLU D:26 , ARG D:27BINDING SITE FOR RESIDUE ACT D 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FKF)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp A:43 -Pro A:44
2Leu A:112 -Pro A:113
3Asp B:43 -Pro B:44
4Leu B:112 -Pro B:113
5Leu C:112 -Pro C:113
6Leu D:112 -Pro D:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FKF)

(-) 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:141
 aligned with Q5L7K1_BACFN | Q5L7K1 from UniProtKB/TrEMBL  Length:356

    Alignment length:141
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343 
         Q5L7K1_BACFN   204 VTVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAMLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 344
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkfA00 A:2-142 Glutaredoxin                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.....ee..........eeeeeeehhhhh.hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh....eee...hhhhhhhhhhh......eeeee.....eeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkf A   2 VTVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAmLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 142
                                    11        21        31        41        51        61     |  71        81        91       101       111       121       131       141 
                                                                                            67-MSE                                                                       


Chain B from PDB  Type:PROTEIN  Length:141
 aligned with Q5L7K1_BACFN | Q5L7K1 from UniProtKB/TrEMBL  Length:356

    Alignment length:141
                                   213       223       233       243       253       263       273       283       293       303       313       323       333       343 
         Q5L7K1_BACFN   204 VTVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAMLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 344
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkfB00 B:2-142 Glutaredoxin                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........ee.....ee..........eeeeeeehhhhh.hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh....eee...hhhhhhhhhhh......eeeee.....eeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkf B   2 VTVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAmLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 142
                                    11        21        31        41        51        61     |  71        81        91       101       111       121       131       141 
                                                                                            67-MSE                                                                       


Chain C from PDB  Type:PROTEIN  Length:140
 aligned with Q5L7K1_BACFN | Q5L7K1 from UniProtKB/TrEMBL  Length:356

    Alignment length:140
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344
         Q5L7K1_BACFN   205 TVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAMLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 344
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkfC00 C:3-142 Glutaredoxin                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.....ee..........eeeeeee......hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh....eeee..hhhhhhhhhhh......eeeee.....eeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkf C   3 TVGKSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAmLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 142
                                    12        22        32        42        52        62    |   72        82        92       102       112       122       132       142
                                                                                           67-MSE                                                                       


Chain D from PDB  Type:PROTEIN  Length:137
 aligned with Q5L7K1_BACFN | Q5L7K1 from UniProtKB/TrEMBL  Length:356

    Alignment length:137
                                   217       227       237       247       257       267       277       287       297       307       317       327       337       
         Q5L7K1_BACFN   208 KSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAMLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 344
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fkfD00 D:6-142 Glutaredoxin                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee.....ee..........eeeeeee.......hhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhh....eeee..hhhhhhhhhhh......eeeee.....eeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fkf D   6 KSAPYFSLPNEKGEKLSRSAERFRNRYLLLNFWASWCDPQPEANAELKRLNKEYKKNKNFAmLGISLDIDREAWETAIKKDTLSWDQVCDFTGLSSETAKQYAILTLPTNILLSPTGKILARDIQGEALTGKLKELL 142
                                    15        25        35        45        55        65 |      75        85        95       105       115       125       135       
                                                                                        67-MSE
   Legend:   → Mismatch (orange background)
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    → 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 3FKF)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3FKF)

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