3VTZ | pdb_00003vtz

Structure of Thermoplasma volcanium aldohexose dehydrogenase

PDB DOI: https://doi.org/10.2210/pdb3VTZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermoplasma volcanium GSS1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-06-12 Released: 2012-07-18
Deposition Author(s): Yasutake, Y., Nishioka, T., Tamura, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.232 (Depositor), 0.228 (DCC)
R-Value Work:
0.167 (Depositor), 0.164 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3VTZ

This is version 1.1 of the entry. See complete history.

Literature

Structure of Thermoplasma volcanium aldohexose dehydrogenase

Yasutake, Y., Nishioka, T., Tamura, T.

To be published.

Macromolecule Content

Total Structure Weight: 116.99 kDa
Atom Count: 7,720
Modeled Residue Count: 1,010
Deposited Residue Count: 1,076
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose 1-dehydrogenase	A, B, C, D	269	Thermoplasma volcanium GSS1	Mutation(s): 0 Gene Names: TV0074 EC: 1.1.1.118
UniProt
Find proteins for Q97CM7 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97CM7 Go to UniProtKB: Q97CM7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97CM7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.232 (Depositor), 0.228 (DCC)
R-Value Work: 0.167 (Depositor), 0.164 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.018	α = 90
b = 110.018	β = 90
c = 77.172	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-07-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-18
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.