3GFG

Structure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form

• PDB DOI: https://doi.org/10.2210/pdb3GFG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-02-26 Released: 2009-03-24 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Gilmore, M., Chang, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 

Literature

Crystal structure of putative oxidoreductase yvaA from Bacillus subtilis in triclinic form.

Ramagopal, U.A., Toro, R., Gilmore, M., Chang, S., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 495.22 kDa 
• Atom Count: 32,457 
• Modelled Residue Count: 4,081 
• Deposited Residue Count: 4,404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase yvaA	A, B, C, D, E, F, G, H, I, J, K, L	367	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: BSU33530, yvaA
UniProt
Find proteins for O32223 (Bacillus subtilis (strain 168)) Explore O32223  Go to UniProtKB:  O32223

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.236 
• R-Value Work: 0.182 
• R-Value Observed: 0.185 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.931	α = 95.31
b = 92.135	β = 94.19
c = 187.589	γ = 95.21

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Ramagopal, U.A., Toro, R., Gilmore, M., Chang, S., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description