3VPZ | pdb_00003vpz

Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A

• PDB DOI: https://doi.org/10.2210/pdb3VPZ/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudoalteromonas sp. AS-131
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-16 Released: 2013-03-20 
• Deposition Author(s): Oda, T., Fuchita, N., Motoshima, H., Kawamoto, M., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A

Oda, T., Fuchita, N., Motoshima, H., Kawamoto, M., Watanabe, K.

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: 35.13 kDa 
• Atom Count: 2,628 
• Modeled Residue Count: 322 
• Deposited Residue Count: 331 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase	A	331	Pseudoalteromonas sp. AS-131	Mutation(s): 0  Gene Names: glk EC: 2.7.1.2
UniProt
Find proteins for H7CHS4 (Pseudoalteromonas sp. AS-131) Explore H7CHS4  Go to UniProtKB:  H7CHS4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.61	α = 90
b = 98.61	β = 90
c = 59.73	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Oda, T., Fuchita, N., Motoshima, H., Kawamoto, M., Watanabe, K.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary