4KA0 | pdb_00004ka0

Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P21221

• PDB DOI: https://doi.org/10.2210/pdb4KA0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phocaeicola vulgatus ATCC 8482
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-04-21 Released: 2013-05-22 
• Deposition Author(s): Vetting, M.W., Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R.D., Bonanno, J.B., Armstrong, R.N., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.270 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.205 (Depositor) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a putative thiol-disulfide oxidoreductase from Bacteroides vulgatus (target NYSGRC-011676), space group P21221

Vetting, M.W., Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R.D., Bonanno, J.B., Armstrong, R.N., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.26 kDa 
• Atom Count: 4,698 
• Modeled Residue Count: 565 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative thiol-disulfide oxidoreductase	A, B, C, D	168	Phocaeicola vulgatus ATCC 8482	Mutation(s): 0  Gene Names: BVU_2222
UniProt
Find proteins for A6L2G8 (Phocaeicola vulgatus (strain ATCC 8482 / DSM 1447 / JCM 5826 / CCUG 4940 / NBRC 14291 / NCTC 11154)) Explore A6L2G8  Go to UniProtKB:  A6L2G8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.270 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.205 (Depositor) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.04	α = 90
b = 90.51	β = 90
c = 96.63	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
MOSFLM	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Vetting, M.W., Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Khafizov, K., Seidel, R.D., Bonanno, J.B., Armstrong, R.N., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary