2OOD | pdb_00002ood

Crystal structure of guanine deaminase from Bradyrhizobium japonicum

• PDB DOI: https://doi.org/10.2210/pdb2OOD/pdb

• Classification: HYDROLASE
• Organism(s): Bradyrhizobium diazoefficiens USDA 110
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-01-25 Released: 2007-02-20 
• Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Literature

Crystal structure of guanine deaminase from Bradyrhizobium japonicum

Agarwal, R., Burley, S.K., Swaminathan, S.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 53.57 kDa 
• Atom Count: 3,939 
• Modelled Residue Count: 463 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Blr3880 protein	A	475	Bradyrhizobium diazoefficiens USDA 110	Mutation(s): 10  Gene Names: bII3846, blr3880 EC: 3.5.4.3
UniProt
Find proteins for Q89NG0 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89NG0  Go to UniProtKB:  Q89NG0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GUN	C [auth A]	GUANINE C5 H5 N5 O UYTPUPDQBNUYGX-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 2.62 Å
• R-Value Free:  0.222 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.216	α = 90
b = 193.216	β = 90
c = 121.54	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Agarwal, R., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references
• Version 1.5: 2024-10-09
  Changes: Structure summary