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- PDB-4y9s: structure of an H300N mutant of potato epoxide hydrolase, StEH1 -

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Basic information

Entry
Database: PDB / ID: 4y9s
Titlestructure of an H300N mutant of potato epoxide hydrolase, StEH1
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / mutation of catalytic residue
Function / homology
Function and homology information


soluble epoxide hydrolase / hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
soluble epoxide hydrolase
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNaworyta, A. / Mowbray, S.L. / Widersten, M.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vetenskapsradet Sweden
CitationJournal: ACS Catal / Year: 2015
Title: Expanding the Catalytic Triad in Epoxide Hydrolases and Related Enzymes.
Authors: Amrein, B.A. / Bauer, P. / Duarte, F. / Janfalk Carlsson, A. / Naworyta, A. / Mowbray, S.L. / Widersten, M. / Kamerlin, S.C.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 10, 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

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Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)74,2632
Polymers74,2632
Non-polymers00
Water8,683482
1
A: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,1321
Polymers37,1321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,1321
Polymers37,1321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.021, 96.036, 121.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epoxide hydrolase


Mass: 37131.508 Da / Num. of mol.: 2 / Mutation: H300N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Plasmid: pGTacStEH1-5H / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q41415
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% ...Details: 1 UL DROPS OF PROTEIN SOLUTION (7.2 MG/ML, I.E. 0.2 MM, IN 30 MM TRIS-HCL, PH 7.4, 5 MM VALPROMIDE) WERE MIXED WITH 1 UL DROPS OF RESERVOIR SOLUTION (CONTAINING 90 MM NA-HEPES, PH 7.5, 25% PEG 10, 000). Once crystals were obtained they were soaked in mother liquor at pH 3.5 prior to freezing.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2008 / Details: toroidal mirror
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→51.36 Å / Num. obs: 45161 / % possible obs: 100 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.8.0073phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJP

2cjp


Resolution: 2→51.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.353 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19873 2276 5 %RANDOM
Rwork0.14696 ---
obs0.14957 42817 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.956 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.53 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2→51.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5111 0 0 482 5593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195271
X-RAY DIFFRACTIONr_bond_other_d0.0010.025011
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9517171
X-RAY DIFFRACTIONr_angle_other_deg0.912311547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88123.917240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81115844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9541520
X-RAY DIFFRACTIONr_chiral_restr0.1170.2763
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7761.7322554
X-RAY DIFFRACTIONr_mcbond_other1.7721.7312553
X-RAY DIFFRACTIONr_mcangle_it2.6122.5873189
X-RAY DIFFRACTIONr_mcangle_other2.6122.5873190
X-RAY DIFFRACTIONr_scbond_it2.8172.0382717
X-RAY DIFFRACTIONr_scbond_other2.8172.0392718
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.42.9163983
X-RAY DIFFRACTIONr_long_range_B_refined6.29515.1616408
X-RAY DIFFRACTIONr_long_range_B_other6.15814.7716243
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 164 -
Rwork0.177 3099 -
obs--100 %

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