3VGM

Crystal structure of a ROK family glucokinase from Streptomyces griseus in complex with glucose

• PDB DOI: https://doi.org/10.2210/pdb3VGM/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces griseus subsp. griseus NBRC 13350
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-08-15 Released: 2011-12-07 
• Deposition Author(s): Miyazono, K., Tabei, N., Morita, S., Ohnishi, Y., Horinouchi, S., Tanokura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.185 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.73 kDa 
• Atom Count: 2,538 
• Modelled Residue Count: 312 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	321	Streptomyces griseus subsp. griseus NBRC 13350	Mutation(s): 0  Gene Names: glkA, SGR_5377 EC: 2.7.1.2
UniProt
Find proteins for B1VZT1 (Streptomyces griseus subsp. griseus (strain JCM 4626 / NBRC 13350)) Explore B1VZT1  Go to UniProtKB:  B1VZT1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.84 Å
• R-Value Free: 0.185 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.19	α = 90
b = 108.19	β = 90
c = 141.18	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Miyazono, K., Tabei, N., Morita, S., Ohnishi, Y., Horinouchi, S., Tanokura, M.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary