4YOD | pdb_00004yod

Crystal structure of a thioredoxin-like protein (BACCAC_02376) from Bacteroides caccae ATCC 43185 at 1.90 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4YOD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacteroides caccae ATCC 43185
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-11 Released: 2015-03-25 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.214 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Crystal structure of a thioredoxin-like protein (BACCAC_02376) from Bacteroides caccae ATCC 43185 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 33.45 kDa 
• Atom Count: 2,476 
• Modeled Residue Count: 277 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
thioredoxin-like protein	A	287	Bacteroides caccae ATCC 43185	Mutation(s): 0  Gene Names: BACCAC_02376

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.214 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3WK5R

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.21	α = 90
b = 45.42	β = 97.42
c = 70.67	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
XDS	data scaling
BUSTER	refinement
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-02-01
  Changes: Database references
• Version 1.4: 2024-10-23
  Changes: Data collection, Structure summary