3Q0G

Crystal Structure of the Mycobacterium tuberculosis Crotonase Bound to a Reaction Intermediate Derived from Crotonyl CoA

PDB DOI: https://doi.org/10.2210/pdb3Q0G/pdb

Classification: LYASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-12-15 Released: 2012-01-25
Deposition Author(s): Bruning, J.B., Delgado, E., Ghosh, S., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.288 (Depositor), 0.320 (DCC)
R-Value Work:
0.233 (Depositor), 0.270 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Prokaryotic Crotonase

Bruning, J.B., Delgado, E., Ghosh, S., Sacchettini, J.C.

To be published.

Macromolecule Content

Total Structure Weight: 165.73 kDa
Atom Count: 12,127
Modelled Residue Count: 1,517
Deposited Residue Count: 1,542
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
enoyl-CoA hydratase echA8	A, B, C, D, E A, B, C, D, E, F	257	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: echA8, MT1100, MTV017.23c, Rv1070c EC: 4.2.1.17
UniProt
Find proteins for P9WNN9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WNN9 Go to UniProtKB: P9WNN9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WNN9
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCO Query on BCO Download Ideal Coordinates CCD File SDF format, chain M [auth F] MOL2 format, chain M [auth F] mmCIF format, chain M [auth F]	M [auth F]	Butyryl Coenzyme A C₂₅ H₄₂ N₇ O₁₇ P₃ S CRFNGMNYKDXRTN-CITAKDKDSA-N		Interactions Focus chain M [auth F] Interactions & Density Focus chain M [auth F]
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth D] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth D] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth D]	H [auth A], I [auth B], K [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth D] Interactions & Density Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain L [auth F]	G [auth A], L [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.288 (Depositor), 0.320 (DCC)
R-Value Work: 0.233 (Depositor), 0.270 (DCC)
R-Value Observed: 0.236 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.64	α = 90
b = 133.17	β = 90
c = 133.69	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-01-25

Deposition Author(s):

TB Structural Genomics Consortium (TBSGC)

Revision History (Full details and data files)

Version 1.0: 2012-01-25
Type: Initial release
Version 1.1: 2015-02-11
Changes: Non-polymer description, Other
Version 1.2: 2016-01-27
Changes: Non-polymer description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description