1VRB | pdb_00001vrb

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VRB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-02-18 Released: 2005-03-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Literature

Crystal structure of Putative asparaginyl hydroxylase (2636534) from Bacillus subtilis at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content 

• Total Structure Weight: 157.36 kDa 
• Atom Count: 9,036 
• Modeled Residue Count: 1,224 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative asparaginyl hydroxylase	A, B, C, D	342	Bacillus subtilis	Mutation(s): 6  Gene Names: yxbC
UniProt
Find proteins for P46327 (Bacillus subtilis (strain 168)) Explore P46327  Go to UniProtKB:  P46327

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	E [auth A], F [auth B], G [auth C], H [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.272 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VRB

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.3	α = 90
b = 104.66	β = 90
c = 286.61	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELXD	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-03-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary