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

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Basic information

Entry
Database: PDB / ID: 8qvk
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 / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / phospholipid dephosphorylation / epoxide metabolic process / lipid phosphatase activity / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / peroxisomal matrix / toxic substance binding / cholesterol homeostasis / Peroxisomal protein import / 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-6N0 / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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

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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)62,3812
Polymers62,0031
Non-polymers3781
Water2,846158
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7624
Polymers124,0052
Non-polymers7572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area4170 Å2
ΔGint-7 kcal/mol
Surface area42880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.43, 95.43, 246.89
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 (butterflies/moths) / References: UniProt: P34913
#2: Chemical ChemComp-6N0 / N-(5,5-dioxodibenzothiophen-2-yl)-4,4-difluoro-piperidine-1-carboxamide


Mass: 378.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16F2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: Rods
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: Jun 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→49.45 Å / Num. obs: 72694 / % possible obs: 100 % / Redundancy: 41.55 % / CC1/2: 0.9424 / Net I/σ(I): 5.96
Reflection shellResolution: 2.1→2.11 Å / Num. unique obs: 7123 / CC1/2: 0.3002
Serial crystallography sample deliveryDescription: silicon nitride membrane (Silson) / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: silicon nitride membrane / Support base: cryo cap

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.182 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.164 / SU Rfree Cruickshank DPI: 0.162
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 2013 -RANDOM
Rwork0.1923 ---
obs0.1943 39762 100 %-
Displacement parametersBiso mean: 56.47 Å2
Baniso -1Baniso -2Baniso -3
1--4.5098 Å20 Å20 Å2
2---4.5098 Å20 Å2
3---9.0196 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 26 158 4472
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084438HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.946031HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1529SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes748HARMONIC5
X-RAY DIFFRACTIONt_it4438HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion565SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3105SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion17.3
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection% reflection
Rfree0.3558 46 -
Rwork0.383 --
obs0.3813 796 100 %

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