5J77 | pdb_00005j77

Mutant glyceraldehyde dehydrogenase (F34M+S405N) from Thermoplasma acidophilum

PDB DOI: https://doi.org/10.2210/pdb5J77/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermoplasma acidophilum DSM 1728
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-04-06 Released: 2017-05-10
Deposition Author(s): Iermak, I., Mesters, J.R., Kuta Smatanova, I.
Funding Organization(s): Czech Academy of Sciences

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.226 (Depositor), 0.234 (DCC)
R-Value Work:
0.176 (Depositor), 0.188 (DCC)
R-Value Observed:
0.178 (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

Structure of wild-type glyceraldehyde dehydrogenase from Thermoplasma acidophilum in complex with NADP

Iermak, I., Mesters, J.R., Steffler, F., Sieber, V., Kuta Smatanova, I.

To be published.

Macromolecule Content

Total Structure Weight: 226.11 kDa
Atom Count: 15,691
Modeled Residue Count: 1,968
Deposited Residue Count: 2,032
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glyceraldehyde dehydrogenase (NADP(+))	A, B, C, D	508	Thermoplasma acidophilum DSM 1728	Mutation(s): 2 Gene Names: Ta0809 EC: 1.2.1.89
UniProt
Find proteins for Q9HK01 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HK01 Go to UniProtKB: Q9HK01
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HK01
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226 (Depositor), 0.234 (DCC)
R-Value Work: 0.176 (Depositor), 0.188 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.071	α = 90
b = 158.423	β = 91.57
c = 130.05	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Kuta Smatanova, I.

Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	DAAD-16-09

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description

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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.