2X8W | pdb_00002x8w

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

• PDB DOI: https://doi.org/10.2210/pdb2X8W/pdb

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


• Deposited: 2010-03-13 Released: 2011-03-23 
• 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: 1.95 Å
• R-Value Free: 
  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Methylglyoxal Synthase from Thermus Sp.Gh5 in the Open and Closed Conformational States Provide Insight Into the Mechanism of Allosteric Regulation

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: 14.47 kDa 
• Atom Count: 1,085 
• Modeled Residue Count: 125 
• Deposited Residue Count: 132 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHYLGLYOXAL SYNTHASE	A	132	Thermus sp. GH5	Mutation(s): 0  EC: 4.2.99.11 (PDB Primary Data), 4.2.3.3 (UniProt)
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
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.223 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.83	α = 90
b = 109.83	β = 90
c = 75.74	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Shahsavar, A., Erfani Moghaddam, M., Antonyuk, S.V., Khajeh, K., Naderi-Manesh, H.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-15
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description