3GM5

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.218

wwPDB Validation 3D Report Full Report

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

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22528
Primary Citation of Related Structures:
3GM5

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8RCQ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.247
R-Value Work: 0.218
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

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Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Revision History (Full details and data files)

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

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3GM5

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)