2XW6 | pdb_00002xw6

The Crystal Structure of Methylglyoxal Synthase from Thermus sp. GH5 Bound to Phosphate Ion.

• PDB DOI: https://doi.org/10.2210/pdb2XW6/pdb

• Classification: LYASE
• Organism(s): Thermus sp. GH5
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-11-01 Released: 2011-11-09 
• Deposition Author(s): Shahsavar, A., Erfani Moghaddam, M., Antonyuk, S.V., Khajeh, K., Naderi-Manesh, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 
  0.161 (Depositor) 
• R-Value Observed: 
  0.129 (Depositor) 

Starting Model: experimental

Literature

Atomic Resolution Structure of Methylglyoxal Synthase from Thermus Sp. Gh5 Bound to Phosphate: Insights Into the Distinctive Effects of Phosphate on the Enzyme Structure

Shahsavar, A., Erfani Moghaddam, M., Antonyuk, S.V., Khajeh, K., Naderi-Manesh, H.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.05 kDa 
• Atom Count: 3,665 
• Modeled Residue Count: 381 
• Deposited Residue Count: 402 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLGLYOXAL SYNTHASE	A, B, C	134	Thermus sp. GH5	Mutation(s): 0  EC: 4.2.3.3
UniProt
Find proteins for B3VH91 (Thermus sp. GH5) Explore B3VH91  Go to UniProtKB:  B3VH91

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free:  0.161 (Depositor) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.636	α = 90
b = 115.172	β = 90
c = 120.431	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Shahsavar, A., Erfani Moghaddam, M., Antonyuk, S.V., Khajeh, K., Naderi-Manesh, H.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.2: 2019-05-22
  Changes: Data collection, Refinement description
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description