2O2H | pdb_00002o2h

Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,2-dichloroethane

• PDB DOI: https://doi.org/10.2210/pdb2O2H/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-11-29 Released: 2007-11-13 
• Deposition Author(s): Mazumdar, P.A., Hulecki, J., Cherney, M.M., Garen, C.R., James, M.N.G., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,2-dichloroethane

Mazumdar, P.A., Hulecki, J., Cherney, M.M., Garen, C.R., James, M.N.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 33.96 kDa 
• Atom Count: 2,579 
• Modeled Residue Count: 294 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Haloalkane dehalogenase 3	A	300	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: dhaA EC: 3.8.1.5
UniProt
Find proteins for P9WMR9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WMR9  Go to UniProtKB:  P9WMR9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCE	D [auth A]	1,2-DICHLOROETHANE C2 H4 Cl2 WSLDOOZREJYCGB-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.12	α = 90
b = 64.46	β = 90
c = 134.21	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-13 
Deposition Author(s): Mazumdar, P.A., Hulecki, J., Cherney, M.M., Garen, C.R., James, M.N.G., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2007-11-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description