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- PDB-1qo7: Structure of Aspergillus niger epoxide hydrolase -

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Basic information

Entry
Database: PDB / ID: 1qo7
TitleStructure of Aspergillus niger epoxide hydrolase
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / EPOXIDE HYDROLASE / ALPHA/BETA HYDROLASE
Function / homology
Function and homology information


epoxide hydrolase / epoxide metabolic process / epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesASPERGILLUS NIGER (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsZou, J.-Y. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A.
CitationJournal: Structure / Year: 2000
Title: Structure of Aspergillus Niger Epoxide Hydrolase at 1.8A Resolution: Implications for the Structure and Function of the Mammalian Microsomal Class of Epoxide Hydrolases
Authors: Zou, J.-Y. / Hallberg, B.M. / Bergfors, T. / Oesch, F. / Arand, M. / Mowbray, S.L. / Jones, T.A.
History
DepositionNov 4, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)88,2482
Polymers88,2482
Non-polymers00
Water6,738374
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-35.6 kcal/mol
Surface area35200 Å2
MethodPQS
Unit cell
Length a, b, c (Å)62.690, 89.320, 75.770
Angle α, β, γ (deg.)90.00, 105.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999, -0.043, -0.022), (-0.048, 0.927, 0.373), (0.005, 0.374, -0.928)
Vector: 58.829, -23.393, 127.74)
DetailsTHE ASYMMETRIC UNIT CONTAINS 1 COPY OF A HOMO-DIMERIC-COMPLEXOF BIOPOLYMERS

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Components

#1: Protein EPOXIDE HYDROLASE / EH


Mass: 44124.180 Da / Num. of mol.: 2 / Fragment: RESIDUES 3-396 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS NIGER (mold) / Strain: LCP521 / Tissue: MYCELIUM
Description: MUSEUM OF NATURAL HISTORY, PARIS, FRANCE. MODIFIED N-TERMINUS
Cellular location: CYTOPLASM / Plasmid: PGEF-ANEH336 / Gene (production host): AJ238460 (EMBL DATABASE ENTRY) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UR30, epoxide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growpH: 6 / Details: 20% PEG6000, 0.1M MES BUFFER PH 6.0, 0.1M NAAC.
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMEDTA1drop
420 mM1dropNaCl
50.02 %sodium azide1drop
620 %PEG60001reservoir
70.1 MMES1reservoir
80.1 Munbuffered sodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.937
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.8→38.3 Å / Num. obs: 74416 / % possible obs: 99.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 5 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 263931
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
SOLVEphasing
CNS0.5refinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1636344.02 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1524 2.1 %RANDOM
Rwork0.224 ---
obs0.224 74309 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.2403 Å2 / ksol: 0.355619 e/Å3
Displacement parametersBiso mean: 23.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.77 Å2
2--3.23 Å20 Å2
3----4.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.24 Å
Luzzati d res low-20 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6128 0 0 374 6502
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.491.5
X-RAY DIFFRACTIONc_mcangle_it0.882
X-RAY DIFFRACTIONc_scbond_it0.582
X-RAY DIFFRACTIONc_scangle_it0.952.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 268 2.2 %
Rwork0.251 11975 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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