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- PDB-4c4x: Crystal structure of human bifunctional epoxide hydroxylase 2 com... -

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Basic information

Entry
Database: PDB / ID: 4c4x
TitleCrystal structure of human bifunctional epoxide hydroxylase 2 complexed with C9
ComponentsBIFUNCTIONAL EPOXIDE HYDROLASE 2
KeywordsHYDROLASE / DRUG DESIGN / MULTIPLE BINDING MODES
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, catalytic domain ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-(3,4-dichlorophenyl)-1,1-dimethyl-urea / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsPilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. ...Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. / Hessler, G. / Wendt, K.-U. / Becker, S. / Griesinger, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: A Combination of Spin Diffusion Methods for the Determination of Protein-Ligand Complex Structural Ensembles.
Authors: Pilger, J. / Mazur, A. / Monecke, P. / Schreuder, H. / Elshorst, B. / Bartoschek, S. / Langer, T. / Schiffer, A. / Krimm, I. / Wegstroth, M. / Lee, D. / Hessler, G. / Wendt, K. / Becker, S. / Griesinger, C.
History
DepositionSep 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Database references
Revision 1.2Jun 10, 2015Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Feb 24, 2021Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_site
Item: _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id ..._pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2084
Polymers74,7422
Non-polymers4662
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint3 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.690, 79.870, 88.610
Angle α, β, γ (deg.)90.00, 89.95, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BIFUNCTIONAL EPOXIDE HYDROLASE 2 / BIFUNCTIONAL EPOXIDE HYDROXYLASE 2 / CYTOSOLIC EPOXIDE HYDROLASE 2 / CEH / EPOXIDE HYDRATASE / ...BIFUNCTIONAL EPOXIDE HYDROXYLASE 2 / CYTOSOLIC EPOXIDE HYDROLASE 2 / CEH / EPOXIDE HYDRATASE / SOLUBLE EPOXIDE HYDROLASE / SEH / LIPID-PHOSPHATE PHOSPHATASE


Mass: 37370.926 Da / Num. of mol.: 2 / Fragment: EPOXIDE HYDROXYLASE DOMAIN RESIDUES 230-555
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-W9M / 3-(3,4-dichlorophenyl)-1,1-dimethyl-urea


Mass: 233.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10Cl2N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: HANGING DROP. 1 UL PROTEIN SOLUTION (8 MG/ML SEH IN 100 MM NAPO2, PH 7.4, 5 MM DTT AND 15% GLYCEROL) WAS MIXED WITH 1 UL RESERVOIR SOLUTION (100 MM TRIS-HCL, PH 8.3, 26% PEG4000 AND 200 MM ...Details: HANGING DROP. 1 UL PROTEIN SOLUTION (8 MG/ML SEH IN 100 MM NAPO2, PH 7.4, 5 MM DTT AND 15% GLYCEROL) WAS MIXED WITH 1 UL RESERVOIR SOLUTION (100 MM TRIS-HCL, PH 8.3, 26% PEG4000 AND 200 MM LI2SO4 AND EQUILIBRATED AT 20C. CRYSTALS APPEARED IN ABOUT 2 WEEKS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→44.31 Å / Num. obs: 35085 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 35.12 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 2.17→2.28 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OTQ

3otq


Resolution: 2.17→29.63 Å / Cor.coef. Fo:Fc: 0.9089 / Cor.coef. Fo:Fc free: 0.879 / SU R Cruickshank DPI: 0.304 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.319 / SU Rfree Blow DPI: 0.211 / SU Rfree Cruickshank DPI: 0.21
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE INHIBITOR HAS BEEN MODELED IN TWO ORIENTATIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 2512 7.21 %RANDOM
Rwork0.2111 ---
obs0.2133 34823 98.8 %-
Displacement parametersBiso mean: 38.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.9696 Å20 Å21.4659 Å2
2--11.5946 Å20 Å2
3----8.625 Å2
Refine analyzeLuzzati coordinate error obs: 0.287 Å
Refinement stepCycle: LAST / Resolution: 2.17→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5061 0 28 445 5534
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075267HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.947141HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1797SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes122HARMONIC2
X-RAY DIFFRACTIONt_gen_planes755HARMONIC5
X-RAY DIFFRACTIONt_it5267HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.13
X-RAY DIFFRACTIONt_other_torsion18.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion629SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6357SEMIHARMONIC4
LS refinement shellResolution: 2.17→2.24 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2635 216 7.22 %
Rwork0.2364 2774 -
all0.2383 2990 -
obs--98.8 %

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