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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.81 Å
R-Value Free:
0.292 (Depositor), 0.293 (DCC)
R-Value Work:
0.245 (Depositor)
R-Value Observed:
0.245 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2AF7

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gamma-carboxymuconolactone decarboxylase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O26336
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E 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), 0.293 (DCC)
R-Value Work: 0.245 (Depositor)
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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2005-08-09

Deposition Author(s):

Montelione, G.T.

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.