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- PDB-4c4z: Crystal structure of human bifunctional epoxide hydroxylase 2 com... -

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Basic information

Entry
Database: PDB / ID: 4c4z
TitleCrystal structure of human bifunctional epoxide hydroxylase 2 complexed with A8
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 / soluble epoxide hydrolase / epoxide metabolic process / 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 / Biosynthesis of maresins / soluble epoxide hydrolase / epoxide metabolic process / 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, 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-ethyl-3-naphthalen-1-ylurea / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.06 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 1.3Feb 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)75,1704
Polymers74,7422
Non-polymers4292
Water10,845602
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint3 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.490, 79.850, 87.220
Angle α, β, γ (deg.)90.00, 89.38, 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-W9L / 1-ethyl-3-naphthalen-1-ylurea


Mass: 214.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 602 / 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: 2.22 Å3/Da / Density % sol: 44.6 % / Description: NONE
Crystal growpH: 8.3 / Details: pH 8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 21, 2012 / Details: OSMIC MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→79.85 Å / Num. obs: 36430 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 21.7
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 8.3 / % possible all: 82.6

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.06→28.67 Å / Cor.coef. Fo:Fc: 0.8927 / Cor.coef. Fo:Fc free: 0.8672 / SU R Cruickshank DPI: 0.317 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.349 / SU Rfree Blow DPI: 0.221 / SU Rfree Cruickshank DPI: 0.216
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2549 7.17 %RANDOM
Rwork0.22 ---
obs0.2223 35547 89.94 %-
Displacement parametersBiso mean: 27.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.9085 Å20 Å2-2.9787 Å2
2--7.8062 Å20 Å2
3----8.7146 Å2
Refine analyzeLuzzati coordinate error obs: 0.323 Å
Refinement stepCycle: LAST / Resolution: 2.06→28.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 32 602 5758
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0075310HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.927200HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1808SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes760HARMONIC5
X-RAY DIFFRACTIONt_it5310HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.03
X-RAY DIFFRACTIONt_other_torsion18.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion640SEMIHARMONIC5
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_contact6643SEMIHARMONIC4
LS refinement shellResolution: 2.06→2.12 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2938 196 7.43 %
Rwork0.2422 2442 -
all0.246 2638 -
obs--89.94 %

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