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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free:
0.248 (Depositor), 0.246 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.204 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of glucokinase from Antarctic psychrotroph at 1.69A

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

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H7CHS4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.69 Å
R-Value Free: 0.248 (Depositor), 0.246 (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

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Entry History

Deposition Data

Released Date: 2013-03-20

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.