2AF7 | pdb_00002af7

Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium target TT747.

• PDB DOI: https://doi.org/10.2210/pdb2AF7/pdb

• Classification: LYASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-07-25 Released: 2005-08-09 
• Deposition Author(s): Vorobiev, S.M., Kuzin, A., Skarina, T., Savchenko, A., Semesi, A., Arrowsmith, C., Edwards, A., Montelione, G.T., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 
  0.292 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Crystal structure of the gamma-carboxymuconolactone decarboxylase from Methanobacterium thermoautotrophicum.

Vorobiev, S.M., Kuzin, A., Skarina, T., Savchenko, A., Semesi, A., Arrowsmith, C., Edwards, A., Montelione, G.T., Tong, L.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 127.98 kDa 
• Atom Count: 8,293 
• Modelled Residue Count: 1,074 
• Deposited Residue Count: 1,125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-carboxymuconolactone decarboxylase	A, B, C, D, E, F, G, H, I	125	Methanothermobacter thermautotrophicus	Mutation(s): 5  Gene Names: MTH234 EC: 4.1.1.44
UniProt
Find proteins for O26336 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O26336  Go to UniProtKB:  O26336

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free:  0.292 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.306	α = 90
b = 119.109	β = 102.8
c = 73.62	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-09 
Deposition Author(s): Vorobiev, S.M., Kuzin, A., Skarina, T., Savchenko, A., Semesi, A., Arrowsmith, C., Edwards, A., Montelione, G.T., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2005-08-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary