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- PDB-4qla: Crystal structure of juvenile hormone epoxide hydrolase from the ... -

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Basic information

Entry
Database: PDB / ID: 4qla
TitleCrystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori
ComponentsJuvenile hormone epoxide hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase / epoxide hydrolase
Function / homology
Function and homology information


microsomal epoxide hydrolase / cis-stilbene-oxide hydrolase activity / : / epoxide metabolic process / catabolic process / endoplasmic reticulum membrane
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
Epoxide hydrolase / Juvenile hormone epoxide hydrolase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhou, K. / Jia, N. / Hu, C. / Jiang, Y.L. / Yang, J.P. / Chen, Y. / Li, S. / Zhou, C.Z.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of juvenile hormone epoxide hydrolase from the silkworm Bombyx mori.
Authors: Zhou, K. / Jia, N. / Hu, C. / Jiang, Y.L. / Yang, J.P. / Chen, Y. / Li, S. / Li, W.F. / Zhou, C.Z.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Juvenile hormone epoxide hydrolase
B: Juvenile hormone epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,4864
Polymers102,0102
Non-polymers4772
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-22 kcal/mol
Surface area32380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.404, 51.466, 124.449
Angle α, β, γ (deg.)90.00, 122.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Juvenile hormone epoxide hydrolase / bommo-JHEH


Mass: 51004.926 Da / Num. of mol.: 2 / Fragment: UNP residues 23-461 / Mutation: D142G, F336L, Y402H, L414M, S433A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Plasmid: pET29a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: H9JWL6, UniProt: Q6U6J0*PLUS, microsomal epoxide hydrolase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, pH 8.0, 19% polyethylene glycol 2000, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 38204 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 32.19 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 11.76
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.88 / Num. unique all: 3671 / Rsym value: 0.5 / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QO7

1qo7


Resolution: 2.3→39.39 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 7.974 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25084 1907 5 %RANDOM
Rwork0.20344 ---
obs0.20587 36297 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.618 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å2-0 Å24.04 Å2
2---2.64 Å20 Å2
3---5.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6491 0 32 159 6682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026712
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0671.979087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80523.785288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.767151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5611529
X-RAY DIFFRACTIONr_chiral_restr0.0790.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215036
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.302→2.362 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 131 -
Rwork0.284 2406 -
obs--92.29 %

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