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- PDB-7a7g: Soluble epoxide hydrolase in complex with TK90 -

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Basic information

Entry
Database: PDB / ID: 7a7g
TitleSoluble epoxide hydrolase in complex with TK90
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 / 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
Similarity search - Domain/homology
Chem-TK9 / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNi, X. / Kramer, J.S. / Kirchner, T. / Proschak, E. / Chaikuad, A. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Combined Cardioprotective and Adipocyte Browning Effects Promoted by the Eutomer of Dual sEH/PPAR gamma Modulator.
Authors: Hartmann, M. / Bibli, S.I. / Tews, D. / Ni, X. / Kircher, T. / Kramer, J.S. / Kilu, W. / Heering, J. / Hernandez-Olmos, V. / Weizel, L. / Scriba, G.K.E. / Krait, S. / Knapp, S. / Chaikuad, A. ...Authors: Hartmann, M. / Bibli, S.I. / Tews, D. / Ni, X. / Kircher, T. / Kramer, J.S. / Kilu, W. / Heering, J. / Hernandez-Olmos, V. / Weizel, L. / Scriba, G.K.E. / Krait, S. / Knapp, S. / Chaikuad, A. / Merk, D. / Fleming, I. / Fischer-Posovszky, P. / Proschak, E.
History
DepositionAug 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)80,1164
Polymers79,2972
Non-polymers8192
Water59433
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint2 kcal/mol
Surface area22960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.808, 79.249, 90.443
Angle α, β, γ (deg.)90.000, 130.620, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 229 - 547 / Label seq-ID: 11 - 329

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39648.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-TK9 / (2~{R})-2-[[4-[[4-methoxy-2-(trifluoromethyl)phenyl]methylcarbamoyl]phenyl]methyl]butanoic acid


Mass: 409.399 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22F3NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.13
Details: 28% PEG6000, 70 mM Ammoniumacetat, 200 mM Magnesium acetat tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.4→39.66 Å / Num. obs: 24408 / % possible obs: 84.7 % / Redundancy: 2.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.071 / Rrim(I) all: 0.111 / Net I/σ(I): 4.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.4920.249510425590.9080.2110.3281.584.6
8.98-39.622.20.04310214550.9910.0360.05711.179.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FR2

6fr2


Resolution: 2.4→39.6 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.914 / SU B: 23.151 / SU ML: 0.242 / SU R Cruickshank DPI: 0.6764 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.676 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 1213 5 %RANDOM
Rwork0.2018 ---
obs0.204 23195 84.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.36 Å2 / Biso mean: 41.333 Å2 / Biso min: 15.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0 Å2-0.68 Å2
2---1.13 Å2-0 Å2
3---0.85 Å2
Refinement stepCycle: final / Resolution: 2.4→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4931 0 58 33 5022
Biso mean--41.06 29.41 -
Num. residues----635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174571
X-RAY DIFFRACTIONr_angle_refined_deg1.1081.647034
X-RAY DIFFRACTIONr_angle_other_deg1.1171.57910567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3645637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.66921.673251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86415783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5051530
X-RAY DIFFRACTIONr_chiral_restr0.0520.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.025979
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021151
Refine LS restraints NCS

Ens-ID: 1 / Number: 10273 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 97 -
Rwork0.277 1652 -
all-1749 -
obs--82.38 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8156-0.7568-0.51691.97021.10861.6529-0.07520.0093-0.09840.1529-0.03960.00760.0878-0.10470.11480.3454-0.0260.04870.0092-0.01430.1026.3584.008722.9487
21.6658-0.1688-1.0892.43370.41561.4041-0.03020.00540.10120.2464-0.07220.1639-0.2374-0.21850.10240.42730.03340.06870.0761-0.07230.1016-1.304815.308727.9497
31.7274-0.5372-0.76291.58151.35242.02230.09420.06280.0925-0.0404-0.0132-0.1614-0.18950.0451-0.0810.30510.00070.04750.00850.01490.138823.7236-4.50463.2493
42.0253-0.0678-1.23111.93550.16522.69350.04020.2011-0.2501-0.1314-0.0551-0.21170.1704-0.00140.01490.25970.03320.09910.0299-0.02280.132627.0981-15.8017-5.3969
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A229 - 368
2X-RAY DIFFRACTION2A369 - 547
3X-RAY DIFFRACTION3B229 - 368
4X-RAY DIFFRACTION4B369 - 547

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