3ON5 | pdb_00003on5

Crystal structure of a xanthine dehydrogenase (BH1974) from Bacillus halodurans at 2.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3ON5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Halalkalibacterium halodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-27 Released: 2010-09-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.222 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a xanthine dehydrogenase (BH1974) from Bacillus halodurans at 2.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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)

Macromolecule Content 

• Total Structure Weight: 83.64 kDa 
• Atom Count: 5,218 
• Modeled Residue Count: 659 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BH1974 protein	A, B	362	Halalkalibacterium halodurans	Mutation(s): 0  Gene Names: 10174592, BH1974
UniProt
Find proteins for Q9KBF4 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KBF4  Go to UniProtKB:  Q9KBF4

Small Molecules

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

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.222 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33ON5

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.244	α = 90
b = 94.244	β = 90
c = 245.536	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
SCALA	data processing
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
Rosetta	phasing
PHASER	phasing
autoSHARP	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-07-20
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Structure summary