1VLW | pdb_00001vlw

Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VLW/pdb

• Classification: LYASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-08-18 Released: 2004-08-24 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase (TM0066) from Thermotoga maritima at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PQS (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.19 kDa 
• Atom Count: 4,770 
• Modeled Residue Count: 616 
• Deposited Residue Count: 651 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase	A, B, C	217	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM0066 EC: 4.1.2.14 (PDB Primary Data), 4.1.3.16 (PDB Primary Data)
UniProt
Find proteins for Q9WXS1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXS1  Go to UniProtKB:  Q9WXS1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VLW

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.543	α = 90
b = 113.194	β = 90
c = 128.397	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: 2004-08-24 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-08-24
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary