1VKE

Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VKE/pdb

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


• Deposited: 2004-05-13 Released: 2004-06-08 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.178 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 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 (software)

Macromolecule Content

• Total Structure Weight: 91.75 kDa 
• Atom Count: 5,473 
• Modelled Residue Count: 635 
• Deposited Residue Count: 798 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
carboxymuconolactone decarboxylase family protein	A, B, C, D, E, F	133	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1620 EC: 4.1
UniProt
Find proteins for Q9X1V5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1V5  Go to UniProtKB:  Q9X1V5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	O [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
UNL	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], P [auth E], Q [auth E], R [auth F], S [auth F]	Unknown ligand SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.178 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VKE

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.922	α = 90
b = 67.975	β = 97.52
c = 90.077	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary