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- PDB-8qmz: Soluble epoxide hydrolase in complex with RK4 -

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Basic information

Entry
Database: PDB / ID: 8qmz
TitleSoluble epoxide hydrolase in complex with RK4
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / COMPLEX / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / 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 / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / 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 / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsKumar, A. / Zhu, F. / Ehrler, J.M.H. / Li, F. / Empel, C. / Xu, Y. / Atodiresei, I. / Koenigs, R.M. / Proschak, E. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)515365930 Germany
German Research Foundation (DFG)448583558 Germany
German Research Foundation (DFG)505561502 Germany
CitationJournal: Science / Year: 2024
Title: Photosensitization enables Pauson-Khand-type reactions with nitrenes.
Authors: Li, F. / Zhu, W.F. / Empel, C. / Datsenko, O. / Kumar, A. / Xu, Y. / Ehrler, J.H.M. / Atodiresei, I. / Knapp, S. / Mykhailiuk, P.K. / Proschak, E. / Koenigs, R.M.
History
DepositionSep 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
B: Bifunctional epoxide hydrolase 2
C: Bifunctional epoxide hydrolase 2
D: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,66724
Polymers167,8044
Non-polymers2,86320
Water15,151841
1
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6676
Polymers41,9511
Non-polymers7165
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7297
Polymers41,9511
Non-polymers7786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5434
Polymers41,9511
Non-polymers5923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7297
Polymers41,9511
Non-polymers7786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.290, 90.642, 188.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Bifunctional epoxide hydrolase 2


Mass: 41951.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli (E. coli)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical
ChemComp-W6O / (3~{a}~{R},6~{a}~{S})-~{N}-[(2,4-dichlorophenyl)methyl]-2-(4-methylphenyl)sulfonyl-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-5-carboxamide


Mass: 467.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C22H24Cl2N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 841 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG6000, 10% ethylene glycol, 0.1M HEPES pH 7.0, 0.1M calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→49.47 Å / Num. obs: 233100 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Χ2: 0.94 / Net I/σ(I): 13.8 / Num. measured all: 1556818
Reflection shellResolution: 1.47→1.49 Å / % possible obs: 91.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.125 / Num. measured all: 72177 / Num. unique obs: 10528 / CC1/2: 0.71 / Rpim(I) all: 0.463 / Rrim(I) all: 1.218 / Χ2: 0.91 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→49.47 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.509 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21408 11504 4.9 %RANDOM
Rwork0.18752 ---
obs0.18882 221479 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.377 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0 Å20 Å2
2--0.69 Å2-0 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.47→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10206 0 184 842 11232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01211079
X-RAY DIFFRACTIONr_bond_other_d0.0010.01610116
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.65715098
X-RAY DIFFRACTIONr_angle_other_deg0.631.57623415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70951363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.632562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.687101800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1110.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213190
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022594
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_it2.0442.0925329
X-RAY DIFFRACTIONr_mcbond_other2.0432.0925329
X-RAY DIFFRACTIONr_mcangle_it2.8743.7596730
X-RAY DIFFRACTIONr_mcangle_other2.8743.766731
X-RAY DIFFRACTIONr_scbond_it3.212.4135750
X-RAY DIFFRACTIONr_scbond_other3.2092.4135751
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.84.3058368
X-RAY DIFFRACTIONr_long_range_B_refined5.93822.1812691
X-RAY DIFFRACTIONr_long_range_B_other5.93822.1812692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.506 Å
RfactorNum. reflection% reflection
Rfree0.331 780 -
Rwork0.305 15363 -
obs--94.11 %

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