5M4X | pdb_00005m4x

Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma acidophilum

• PDB DOI: https://doi.org/10.2210/pdb5M4X/pdb

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


• Deposited: 2016-10-19 Released: 2017-12-20 
• Deposition Author(s): Iermak, I., Mesters, J.R., Kuta Smatanova, I.
• Funding Organization(s): Czech Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.56 Å
• R-Value Free: 
  0.319 (Depositor), 0.330 (DCC) 
• R-Value Work: 
  0.312 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.312 (Depositor) 

Starting Model: experimental

Literature

Mutant glyceraldehyde dehydrogenase (F34M+Y399C+S405N) from Thermoplasma acidophilum

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 225.87 kDa 
• Atom Count: 13,897 
• Modeled Residue Count: 1,862 
• Deposited Residue Count: 2,032 
• Unique protein chains: 1

Macromolecules

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): 3  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.56 Å
• R-Value Free:  0.319 (Depositor), 0.330 (DCC) 
• R-Value Work:  0.312 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.312 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.292	α = 90
b = 120.292	β = 90
c = 344.884	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Iermak, I., Mesters, J.R., Kuta Smatanova, I.

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

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description