3OQB | pdb_00003oqb

CRYSTAL STRUCTURE OF putative oxidoreductase from Bradyrhizobium japonicum USDA 110

• PDB DOI: https://doi.org/10.2210/pdb3OQB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bradyrhizobium diazoefficiens USDA 110
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-09-02 Released: 2010-09-15 
• Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., 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: 2.60 Å
• R-Value Free: 
  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

CRYSTAL STRUCTURE OF putative oxidoreductase from Bradyrhizobium japonicum USDA 110

Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 349.26 kDa 
• Atom Count: 24,247 
• Modeled Residue Count: 3,017 
• Deposited Residue Count: 3,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxidoreductase	A, B, C, D, E, F, G, H	383	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 0  Gene Names: BAC48105.1, blr2840
UniProt
Find proteins for Q89RD2 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89RD2  Go to UniProtKB:  Q89RD2

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D, E, F, G, H	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.247 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.705	α = 90
b = 163.853	β = 103.85
c = 117.726	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Malashkevich, V.N., Toro, R., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-10-30
  Changes: Data collection, Database references, Structure summary