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- PDB-4c4y: Crystal structure of human bifunctional epoxide hydroxylase 2 com... -

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Basic information

Entry
Database: PDB / ID: 4c4y
TitleCrystal structure of human bifunctional epoxide hydroxylase 2 complexed with A4
ComponentsBIFUNCTIONAL EPOXIDE HYDROLASE 2
KeywordsHYDROLASE / DRUG DESIGN
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
1-(3-chlorophenyl)-3-(2-methoxyethyl)urea / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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_oper_list / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Mar 31, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.7Dec 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6002
Polymers37,3711
Non-polymers2291
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.640, 46.340, 80.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

21A-2009-

HOH

31A-2013-

HOH

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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 / BIFUNCTIONAL EPOXIDE HYDROXYLASE 2


Mass: 37370.926 Da / Num. of mol.: 1 / Fragment: EPOXIDE HYDROXYLASE DOMAIN, RESIDUES 230-255
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-7WI / 1-(3-chlorophenyl)-3-(2-methoxyethyl)urea


Mass: 228.675 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13ClN2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.11 Å3/Da / Density % sol: 41.7 % / 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 6M / Detector: PIXEL / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.41→57.24 Å / Num. obs: 12191 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 42.14 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15
Reflection shellResolution: 2.41→2.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.6 / % possible all: 97.8

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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: 2.41→40.82 Å / Cor.coef. Fo:Fc: 0.8444 / Cor.coef. Fo:Fc free: 0.7755 / SU R Cruickshank DPI: 0.957 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.798 / SU Rfree Blow DPI: 0.37 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.3148 579 4.86 %RANDOM
Rwork0.2581 ---
obs0.2608 11906 96.82 %-
Displacement parametersBiso mean: 37.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.1279 Å20 Å20 Å2
2---11.2022 Å20 Å2
3---10.0743 Å2
Refine analyzeLuzzati coordinate error obs: 0.477 Å
Refinement stepCycle: LAST / Resolution: 2.41→40.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 15 139 2689
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0072626HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933558HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d900SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes376HARMONIC5
X-RAY DIFFRACTIONt_it2626HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion19.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion315SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2999SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.64 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4338 137 5.27 %
Rwork0.3797 2461 -
all0.3827 2598 -
obs--96.82 %

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