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- PDB-6hgv: Soluble epoxide hydrolase in complex with talinolol -

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Basic information

Entry
Database: PDB / ID: 6hgv
TitleSoluble epoxide hydrolase in complex with talinolol
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Inhibitor / Complex / sEH
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
R-Talinolol / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKramer, J.S. / Pogoryelov, D. / Hiesinger, K. / Proschak, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Else Kroener Fresenius Stiftung TRIP Graduate School Germany
CitationJournal: Acs Med.Chem.Lett. / Year: 2019
Title: Computer-Aided Selective Optimization of Side Activities of Talinolol.
Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, ...Authors: Hiesinger, K. / Kramer, J.S. / Achenbach, J. / Moser, D. / Weber, J. / Wittmann, S.K. / Morisseau, C. / Angioni, C. / Geisslinger, G. / Kahnt, A.S. / Kaiser, A. / Proschak, A. / Steinhilber, D. / Pogoryelov, D. / Wagner, K. / Hammock, B.D. / Proschak, E.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Jan 17, 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
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)40,0363
Polymers39,6491
Non-polymers3882
Water2,684149
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0736
Polymers79,2972
Non-polymers7764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)79.730, 91.880, 106.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39648.531 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-G3Q / R-Talinolol / Talinolol


Mass: 363.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33N3O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant ...Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant solution (23 %-28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.1-6.5)
PH range: 6.0-6.55

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2017
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.99→45.94 Å / Num. obs: 26999 / % possible obs: 99.6 % / Redundancy: 13.06 % / Biso Wilson estimate: 38.12 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.076 / Χ2: 1.05 / Net I/σ(I): 20.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.0411.980.8862.6519170.8540.92595.1
2.04-2.113.3660.6823.8419100.940.709100
2.1-2.1613.1960.5364.9218780.9640.55899.9
2.16-2.2212.8260.4286.0218040.9770.446100
2.22-2.312.2440.3177.7917940.9870.331100
2.3-2.3813.7060.2649.8417020.990.27599.9
2.38-2.4713.780.21611.7116530.9940.224100
2.47-2.5713.6850.17613.9615830.9950.183100
2.57-2.6813.6370.14117.4915410.9960.147100
2.68-2.8113.2110.11720.0314530.9970.122100
2.81-2.9612.360.09623.8414040.9980.1100
2.96-3.1413.8530.07731.2613150.9980.08100
3.14-3.3613.690.06735.4312610.9990.07100
3.36-3.6313.4640.05641.9511700.9990.058100
3.63-3.9812.8780.05244.4610700.9990.054100
3.98-4.4511.710.04745.59880.9990.04999.9
4.45-5.1313.3560.04450.278680.9990.04699.9
5.13-6.2912.9320.04747.887510.9990.049100
6.29-8.8911.4530.04147.115900.9990.04399.7
8.89-45.9412.210.0452.733470.9990.04198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FR2

6fr2


Resolution: 2→45.94 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.81
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 1698 6.37 %Random selection
Rwork0.1744 ---
obs0.1762 26655 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 159.35 Å2 / Biso mean: 51.5384 Å2 / Biso min: 24.06 Å2
Refinement stepCycle: final / Resolution: 2→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 53 149 2759
Biso mean--78.82 55.19 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052763
X-RAY DIFFRACTIONf_angle_d0.8063760
X-RAY DIFFRACTIONf_chiral_restr0.047385
X-RAY DIFFRACTIONf_plane_restr0.004484
X-RAY DIFFRACTIONf_dihedral_angle_d24.5471028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.05890.28661370.256520222159
2.0589-2.12530.27821420.225720812223
2.1253-2.20130.2511370.199220362173
2.2013-2.28940.20091400.184720472187
2.2894-2.39360.23881410.186220662207
2.3936-2.51980.21041420.189120822224
2.5198-2.67770.22591380.190120472185
2.6777-2.88440.25561430.191820912234
2.8844-3.17460.21441400.183220602200
3.1746-3.63380.18821430.165121072250
3.6338-4.57760.16521440.140521052249
4.5776-45.95210.19261510.174722132364
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)
14.36562.489-0.39255.12710.98825.0314-0.09530.03370.4166-0.34680.04760.0952-0.10950.09240.03210.2292-0.00150.0090.25130.03430.2695-5.5888-6.5224-36.596
22.79610.4317-0.49152.3847-0.06141.5108-0.0699-0.1184-0.315-0.10710.0088-0.33980.22770.1310.04740.25740.00620.02970.27780.01230.3087-3.4475-16.5148-31.3965
37.1547-2.69470.99037.263-2.9187.8182-0.4029-0.0857-1.347-0.24580.38430.28990.8933-0.4793-0.07120.7352-0.11830.11520.4208-0.04080.6229-13.2422-31.2588-44.8105
49.82994.0996-6.57034.7601-3.39634.53-0.1918-0.1028-0.6035-0.5255-0.00840.26830.5814-0.07920.27850.4348-0.0623-0.08530.37310.01820.4124-25.1374-18.9414-43.4814
58.9021-6.0147-2.79894.36182.72153.04270.6287-0.2206-2.3503-0.45860.03411.12641.172-0.6934-0.77971.0873-0.3259-0.28570.7924-0.05521.1069-24.5679-28.2878-48.4051
62.46-0.0941-0.10532.2774-0.12642.0325-0.0930.0018-0.2564-0.18640.0292-0.14580.2072-0.02980.06140.3339-0.0450.03320.26460.00910.3285-11.4963-22.4334-34.6362
75.527-3.99725.43996.2155-4.1995.57820.0052-0.5257-0.156-0.02290.09490.22770.4666-0.2571-0.13880.3564-0.03550.05460.42360.06380.3043-17.2229-20.4578-24.0434
84.5527-2.94454.41559.6806-2.12684.3653-0.1589-1.21620.14510.9870.32150.1081-0.4761-0.4778-0.09810.36640.02630.0660.4547-0.03930.2307-14.7164-10.6007-18.9328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 270 )A229 - 270
2X-RAY DIFFRACTION2chain 'A' and (resid 271 through 370 )A271 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 399 )A371 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 418 )A400 - 418
5X-RAY DIFFRACTION5chain 'A' and (resid 419 through 435 )A419 - 435
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 509 )A436 - 509
7X-RAY DIFFRACTION7chain 'A' and (resid 510 through 530 )A510 - 530
8X-RAY DIFFRACTION8chain 'A' and (resid 531 through 547 )A531 - 547

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