3GM5 | pdb_00003gm5

Crystal structure of a putative methylmalonyl-coenzyme A epimerase from Thermoanaerobacter tengcongensis at 2.0 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GM5/pdb

• Classification: ISOMERASE
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-03-12 Released: 2009-09-22 
• Deposition Author(s): Liang, D.-C., Shi, L., Gao, P., Yan, X.-X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 

Literature

Crystal structure of a putative methylmalonyl-coenzyme a epimerase from Thermoanaerobacter tengcongensis at 2.0 A resolution

Shi, L., Gao, P., Yan, X.-X., Liang, D.-C.

(2009) Proteins 77: 994-999

• PubMed: 19731367 
• DOI: https://doi.org/10.1002/prot.22528
• Primary Citation Related Structures: 
  3GM5

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 19.16 kDa 
• Atom Count: 1,399 
• Modeled Residue Count: 151 
• Deposited Residue Count: 159 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase and related lyases	A	159	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0  Gene Names: GloA, TTE0360 EC: 5.1.99.1
UniProt
Find proteins for Q8RCQ6 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RCQ6  Go to UniProtKB:  Q8RCQ6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.022	α = 90
b = 54.022	β = 90
c = 104.798	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-22 
Deposition Author(s): Liang, D.-C., Shi, L., Gao, P., Yan, X.-X.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-04
  Changes: Data collection
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations