4HC8 | pdb_00004hc8

CRYSTAL STRUCTURE OF PROBABLE ENOYL-CoA HYDRATASE ECHA3 (Rv0632c, NYSGRC-019494) from Mycobacterium Tuberculosis H37Rv

• PDB DOI: https://doi.org/10.2210/pdb4HC8/pdb

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


• Deposited: 2012-09-28 Released: 2012-10-24 
• Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: other

Literature

Crystal structure of probable enoyl-CoA hydratase ECHA3 (Rv0632c, NYSGRC-019494) from Mycobacterium Tuberculosis H37Rv

Sampathkumar, P., Ahmed, M., Banu, N., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Fiser, A., Gizzi, A., Glenn, A.S., Hammonds, J., Hillerich, B., Khafizov, K., Lafleur, J., Love, J.D., Stead, M., Seidel, R., Toro, R., Almo, S.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)

Macromolecule Content 

• Total Structure Weight: 56.22 kDa 
• Atom Count: 3,609 
• Modeled Residue Count: 467 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enoyl-CoA hydratase/isomerase family protein	A, B	255	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: echA3, MT0660, Rv0632c EC: 4.2.1.17
UniProt
Find proteins for I6Y8B5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y8B5  Go to UniProtKB:  I6Y8B5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth B], H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.249 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.883	α = 90
b = 154.883	β = 90
c = 154.883	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction
SCALEPACK	data scaling
SHELX	phasing
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-24 
Deposition Author(s): Sampathkumar, P., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-10-24
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary