4GIB

2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb4GIB/pdb

• Classification: ISOMERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-08 Released: 2012-08-22 
• Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.259 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

2.27 Angstrom Crystal Structure of beta-Phosphoglucomutase (pgmB) from Clostridium difficile.

Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Papazisi, L., Anderson, W.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.17 kDa 
• Atom Count: 3,826 
• Modelled Residue Count: 448 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-phosphoglucomutase	A, B	250	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_21890, pgmB EC: 5.4.2.6
UniProt
Find proteins for Q185X7 (Clostridioides difficile (strain 630)) Explore Q185X7  Go to UniProtKB:  Q185X7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	E [auth A], F [auth A], G [auth A], K [auth B], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY	H [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
NA	C [auth A], D [auth A], I [auth B], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.259 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m34gib

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.807	α = 90
b = 51.364	β = 112.04
c = 79.442	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Minasov, G., Halavaty, A., Shuvalova, L., Dubrovska, I., Winsor, J., Grimshaw, S., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description