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- PDB-2zjf: Crystal structure of Mycobacterium tuberculosis epoxide hydrolase... -

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Basic information

Entry
Database: PDB / ID: 2zjf
TitleCrystal structure of Mycobacterium tuberculosis epoxide hydrolase B complexed with an inhibitor
ComponentsProbable epoxide hydrolase ephB
KeywordsHYDROLASE / Hydrolase fold / Inhibitor / Enzyme mechanism / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


epoxide hydrolase B activity / soluble epoxide hydrolase / response to toxic substance / protein homodimerization activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,3-DIPHENYLUREA / Epoxide hydrolase B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBiswal, B.K. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor.
Authors: Biswal, B.K. / Morisseau, C. / Garen, G. / Cherney, M.M. / Garen, C. / Niu, C. / Hammock, B.D. / James, M.N.
History
DepositionMar 7, 2008Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 9, 2012Group: Structure summary
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable epoxide hydrolase ephB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5235
Polymers40,1341
Non-polymers3894
Water2,162120
1
A: Probable epoxide hydrolase ephB
hetero molecules

A: Probable epoxide hydrolase ephB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,04710
Polymers80,2682
Non-polymers7798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.415, 66.415, 156.829
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Probable epoxide hydrolase ephB / Epoxide hydratase / Epoxide hydrolase


Mass: 40133.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: ephB, MT1988, Rv1938 / Plasmid: pDEST17_Rv1938 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P95276, soluble epoxide hydrolase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BSU / 1,3-DIPHENYLUREA / DIPHENYLCARBAMIDE / 1,3-Diphenylurea


Mass: 212.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N2O / Comment: hormone*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% Isopropanol, 0.2 M CaCl2, 0.1 M Sodium acetate buffer, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 14465 / Num. obs: 14465 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.127 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.57 / % possible all: 99.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EK1

1ek1


Resolution: 2.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 724 -Random
Rwork0.202 ---
all0.202 14403 --
obs0.202 14403 99.7 %-
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.47 Å20 Å20 Å2
2--10.47 Å20 Å2
3----20.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 28 120 2856
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033
RfactorNum. reflection% reflection
Rfree0.356 117 -
Rwork0.297 --
obs-2200 98.6 %

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