3NAS | pdb_00003nas

The crystal structure of beta-phosphoglucomutase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3NAS/pdb

• Classification: ISOMERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-02 Released: 2010-07-28 
• Deposition Author(s): Zhang, Z., 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: 3.00 Å
• R-Value Free: 
  0.290 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

The crystal structure of beta-phosphoglucomutase from Bacillus subtilis

Zhang, Z., 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 (software)

Macromolecule Content 

• Total Structure Weight: 52.57 kDa 
• Atom Count: 3,117 
• Modeled Residue Count: 412 
• Deposited Residue Count: 466 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-phosphoglucomutase	A, B	233	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU34550, yvdM EC: 5.4.2.6
UniProt
Find proteins for O06995 (Bacillus subtilis (strain 168)) Explore O06995  Go to UniProtKB:  O06995

Small Molecules

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: 3.00 Å
• R-Value Free:  0.290 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.233 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.043	α = 90
b = 78.171	β = 90
c = 92.067	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SOLVE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Zhang, Z., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary