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- PDB-8qvh: Comparison of room-temperature and cryogenic structures of solubl... -

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Basic information

Entry
Database: PDB / ID: 8qvh
TitleComparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Inhibitor / serial crystallography / drug discovery / fixed target / room temperature / microcrystals
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / Peroxisomal protein import / regulation of cell growth / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-AUB / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsDunge, A. / Uwangue, O. / Phan, C. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G.
Funding support Sweden, 4items
OrganizationGrant numberCountry
The Swedish Foundation for Strategic ResearchID17-0060 Sweden
Swedish Research Council2017-06734 Sweden
Swedish Research Council2021-05662 Sweden
Swedish Research Council2021-05981 Sweden
CitationJournal: Iucrj / Year: 2024
Title: Exploring serial crystallography for drug discovery.
Authors: Dunge, A. / Phan, C. / Uwangue, O. / Bjelcic, M. / Gunnarsson, J. / Wehlander, G. / Kack, H. / Branden, G.
History
DepositionOct 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4152
Polymers62,0031
Non-polymers4131
Water3,315184
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,8304
Polymers124,0052
Non-polymers8252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area4360 Å2
ΔGint-4 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.41, 95.41, 244.29
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 62002.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34913
#2: Chemical ChemComp-AUB / 4-[(trans-4-{[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbamoyl]amino}cyclohexyl)oxy]benzoic acid


Mass: 412.522 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H32N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: batch mode
Details: 32-42% PEG 3350, 0.1M Li2SO4 and 0.1M Tris-HCl (pH 8.2)

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.24→49.11 Å / Num. obs: 61484 / % possible obs: 100 % / Redundancy: 93.32 % / CC1/2: 0.9886 / Net I/σ(I): 6.22
Reflection shellResolution: 2.24→2.25 Å / Num. unique obs: 2056 / CC1/2: 0.4365
Serial crystallography sample deliveryDescription: silicon nitride membrane (Silson) / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon nitride membrane

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→49.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.25 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1625 -RANDOM
Rwork0.1873 ---
obs0.1894 32577 100 %-
Displacement parametersBiso mean: 45.23 Å2
Baniso -1Baniso -2Baniso -3
1--5.0911 Å20 Å20 Å2
2---5.0911 Å20 Å2
3---10.1823 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.24→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4307 0 30 184 4521
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084459HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.966051HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1543SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes744HARMONIC5
X-RAY DIFFRACTIONt_it4459HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion564SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3168SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.15
X-RAY DIFFRACTIONt_other_torsion18.29
LS refinement shellResolution: 2.24→2.25 Å
RfactorNum. reflection% reflection
Rfree0.2861 26 -
Rwork0.3633 --
obs0.3601 652 100 %

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