3Q0G | pdb_00003q0g

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)

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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

Literature

Crystal Structure of the Prokaryotic Crotonase

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
enoyl-CoA hydratase echA8	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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BCO	M [auth F]	Butyryl Coenzyme A C25 H42 N7 O17 P3 S CRFNGMNYKDXRTN-CITAKDKDSA-N
COA	J [auth C]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
GOL	H [auth A], I [auth B], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	G [auth A], L [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Entry History 

Deposition Data

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

Revision History  

• 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