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- PDB-2e3j: The crystal structure of epoxide hydrolase B (Rv1938) from mycoba... -

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Basic information

Entry
Database: PDB / ID: 2e3j
TitleThe crystal structure of epoxide hydrolase B (Rv1938) from mycobacterium tuberculosis at 2.1 angstrom
ComponentsEPOXIDE HYDROLASE EPHB
KeywordsHYDROLASE / EPOXIDE HYDROLASE B / MYCOBACTERIUM TUBERCULOSIS / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


: / 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 / Epoxide hydrolase B
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBiswal, B.K. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
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
DepositionNov 27, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 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: EPOXIDE HYDROLASE EPHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,83710
Polymers39,3051
Non-polymers5319
Water2,306128
1
A: EPOXIDE HYDROLASE EPHB
hetero molecules

A: EPOXIDE HYDROLASE EPHB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,67320
Polymers78,6102
Non-polymers1,06318
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)66.258, 66.258, 157.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2091-

HOH

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Components

#1: Protein EPOXIDE HYDROLASE EPHB / EPOXIDE HYDROLASE B / EPOXIDE HYDRATASE / Epoxide hydrolase


Mass: 39305.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Plasmid: PDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (AI) / References: UniProt: P95276, epoxide hydrolase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% 2-PROPANOL, 0.2M CaCl2, 0.1M sodium acetate buffer, protein concentration 5-10mg/ml, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.1→39.28 Å / Num. all: 21248 / Num. obs: 20701 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 35.8 Å2 / Rsym value: 0.07
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 1663 / Rsym value: 0.492 / % possible all: 80.4

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RESIDUES 245-541 (C-TREMINAL DOMAIN) of PDB ID 1EK1

1ek1


Resolution: 2.1→39.28 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 1038 -RANDOM
Rwork0.235 ---
all-21248 --
obs-20701 97.4 %-
Displacement parametersBiso mean: 52.65 Å2
Baniso -1Baniso -2Baniso -3
1-12.28 Å20 Å20 Å2
2--12.28 Å20 Å2
3----24.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2708 0 36 128 2872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.26
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.032
RfactorNum. reflection% reflection
Rfree0.391 149 -
Rwork0.39 --
obs-2936 84.8 %

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