1VMD

Crystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VMD/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-09-20 Released: 2004-09-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.219 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Crystal structure of Methylglyoxal synthase (TM1185) from Thermotoga maritima at 2.06 A resolution

Joint Center for Structural Genomics (JCSG)

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 41.43 kDa 
• Atom Count: 2,709 
• Modelled Residue Count: 312 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylglyoxal synthase	A, B	178	Thermotoga maritima	Mutation(s): 0  Gene Names: mgsA, TM1185 EC: 4.2.3.3
UniProt
Find proteins for Q9X0R7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0R7  Go to UniProtKB:  Q9X0R7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.219 
• R-Value Work: 0.167 
• R-Value Observed: 0.170 
• Space Group: I 2 3
• Diffraction Data: https://doi.org/10.18430/M31VMD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.243	α = 90
b = 130.243	β = 90
c = 130.243	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-09-28
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description