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- PDB-4ocz: Crystal structure of human soluble epoxide hydrolase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4ocz
TitleCrystal structure of human soluble epoxide hydrolase complexed with 1-(1-isobutyrylpiperidin-4-yl)-3-(4-(trifluoromethyl)phenyl)urea
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / domain-swapped dimer / HYDROLASE-HYDROLASE INHIBITOR complex
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 / peroxisomal matrix / phosphatase activity / toxic substance binding / dephosphorylation / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / hydrolase activity / 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 / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / HAD superfamily/HAD-like ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / DNA polymerase; domain 1 / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2RU / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsLee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morriseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. ...Lee, K.S.S. / Liu, J. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morriseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C. / Nguyen, L. / Wullf, H. / Eldin, M.L. / Mara, A.A. / Newcomer, M.E. / Zeldin, D.C. / Hammock, B.D.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Optimized inhibitors of soluble epoxide hydrolase improve in vitro target residence time and in vivo efficacy.
Authors: Lee, K.S. / Liu, J.Y. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C.A. / Nguyen, L.V. / Hwang, S.H. / Edin, M.L. / Mara, A.A. ...Authors: Lee, K.S. / Liu, J.Y. / Wagner, K.M. / Pakhomova, S. / Dong, H. / Morisseau, C. / Fu, S.H. / Yang, J. / Wang, P. / Ulu, A. / Mate, C.A. / Nguyen, L.V. / Hwang, S.H. / Edin, M.L. / Mara, A.A. / Wulff, H. / Newcomer, M.E. / Zeldin, D.C. / Hammock, B.D.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1624
Polymers62,6861
Non-polymers4773
Water724
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3258
Polymers125,3712
Non-polymers9536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5110 Å2
ΔGint-51 kcal/mol
Surface area43690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.229, 92.229, 243.373
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Bifunctional epoxide hydrolase 2 / Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid- ...Cytosolic epoxide hydrolase 2 / CEH / Epoxide hydratase / Soluble epoxide hydrolase / SEH / Lipid-phosphate phosphatase


Mass: 62685.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Plasmid: ACHSEH1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-2RU / 1-[1-(2-methylpropanoyl)piperidin-4-yl]-3-[4-(trifluoromethyl)phenyl]urea


Mass: 357.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22F3N3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG3350, 0-10% sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012
RadiationMonochromator: Cryo-cooled double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.94→75.89 Å / Num. all: 13582 / Num. obs: 13582 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 71 Å2 / Rsym value: 0.093 / Net I/σ(I): 15.3
Reflection shellResolution: 2.94→3.1 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 1891 / Rsym value: 0.656 / % possible all: 97.1

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S8O
Resolution: 2.94→40 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 46.981 / SU ML: 0.391 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26918 671 5 %RANDOM
Rwork0.18724 ---
all0.19129 12871 --
obs0.19129 12871 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.371 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å22.2 Å20 Å2
2--4.4 Å2-0 Å2
3----6.61 Å2
Refinement stepCycle: LAST / Resolution: 2.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 31 4 4367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194473
X-RAY DIFFRACTIONr_bond_other_d0.0020.023081
X-RAY DIFFRACTIONr_angle_refined_deg1.8011.9776057
X-RAY DIFFRACTIONr_angle_other_deg0.98137523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4235547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.73224.197193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.9215780
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6591526
X-RAY DIFFRACTIONr_chiral_restr0.090.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214906
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02895
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: 2.94→3.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.431 45 -
Rwork0.307 765 -
obs-765 96.54 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.7745-0.81080.81564.3448-1.04310.8919-0.08990.02120.0475-0.70440.03950.0801-0.0616-0.05060.05040.236-0.02710.01850.4003-0.02210.106817.64262.782-7.462
20.43560.3209-0.13671.0651-0.78561.3869-0.03930.08380.0718-0.08190.08950.0534-0.0305-0.0221-0.05030.0457-0.0088-0.01170.1199-0.06230.070520.66539.5655.478
30.3817-0.9346-0.1943.0973-1.14345.87830.01650.1399-0.2751-0.130.21770.59810.8445-1.2391-0.23420.3728-0.0228-0.02810.455-0.11570.385121.1574.81913.383
42.4637-0.7856-0.81991.32240.09592.1054-0.07040.1509-0.2221-0.0844-0.00930.11030.2684-0.11630.07980.1086-0.0494-0.03290.0895-0.04710.088614.25416.77914.604
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 68
2X-RAY DIFFRACTION2A69 - 369
3X-RAY DIFFRACTION3A370 - 420
4X-RAY DIFFRACTION4A421 - 548

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