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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDOREDUCTASE DSBA FROM XYLELLA FASTIDIOSA
 
Authors :  F. C. Rinaldi, B. G. Guimaraes
Date :  26 Sep 07  (Deposition) - 07 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,T
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C,T  (1x)
Keywords :  Disulfide Oxidoreductase, Dsba, Thioredoxin Fold, Redox- Active Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. C. Rinaldi, B. G. Guimaraes
Residues Substitution In The Active Site Of Dsba May Compensate For The Lack Of The Canonical Motif Cphc
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DISULFIDE OXIDOREDUCTASE
    Chains: A, B, C
    EC Number: 1.8.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: XF1436
    Organism Scientific: XYLELLA FASTIDIOSA
    Organism Taxid: 2371
 
Molecule 2 - 8 RESIDUE PEPTIDE
    Chains: T
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: C43(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: XYLELLA FASTIDIOSA
    Organism Taxid: 2371
    Other Details: CHAIN T IS DERIVED FROM THE EXPRESSION SYSTEM THAT WAS CO-PURIFIED WITH THE PROTEIN (XFDSBA)

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCT
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   CT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1UNK8Mod. Amino Acid
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1UNK-1Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 2REM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Thr A:157 -Pro A:158
2Thr B:157 -Pro B:158
3Thr C:157 -Pro C:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2REM)

(-) Exons   (0, 0)

(no "Exon" information available for 2REM)

(-) 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:190
 aligned with Q9PDE3_XYLFA | Q9PDE3 from UniProtKB/TrEMBL  Length:193

    Alignment length:190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
         Q9PDE3_XYLFA     3 HLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAASHG 192
               SCOP domains d2rema_ A: automated matches                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.............eeeeeee...hhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rem A   4 HLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAASHG 193
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with Q9PDE3_XYLFA | Q9PDE3 from UniProtKB/TrEMBL  Length:193

    Alignment length:187
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       
         Q9PDE3_XYLFA     3 HLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAA 189
               SCOP domains d2remb_ B: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.............eeeeeee...hhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee...eee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rem B   4 HLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAA 190
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       


Chain C from PDB  Type:PROTEIN  Length:191
 aligned with Q9PDE3_XYLFA | Q9PDE3 from UniProtKB/TrEMBL  Length:193

    Alignment length:191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191 
         Q9PDE3_XYLFA     2 NHLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAASHG 192
               SCOP domains d2remc_ C: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------Thioredoxin_4-2remC01 C:23-181                                                                                                                                 ------------ Pfam domains (1)
           Pfam domains (2) --------------------Thioredoxin_4-2remC02 C:23-181                                                                                                                                 ------------ Pfam domains (2)
           Pfam domains (3) --------------------Thioredoxin_4-2remC03 C:23-181                                                                                                                                 ------------ Pfam domains (3)
         Sec.struct. author .........eee.............eeeeeee...hhhhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.eeee...eee...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rem C   3 NHLPVVGEDYVEIPDGRPFAPLAGKIEVVEIFGYTCPHCAHFDSKLQAWGARQAKDVRFTLVPAVFGGVWDPFARAYLAADVLGVAKRSHTAMFEAIHEKGSVPIQNVGPDELAVFYAGYGVQPDRFVATFNGPEVEKRFQAARAYALKVRPVGTPTIVVNGRYMVTGHDFEDTLRITDYLVSRERAASHG 193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 


Chain T from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ...ee... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 2rem T   2 xxxxxxxx   9
                            ||||||||
                            2-UNK|||
                             3-UNK||
                              4-UNK|
                               5-UNK
                                6-UNK
                                 7-UNK
                                  8-UNK
                                   9-UNK
   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, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2REM)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Thioredoxin (367)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q9PDE3_XYLFA | Q9PDE3)
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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