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- PDB-3cxu: Structure of a Y149F mutant of epoxide hydrolase from Solanum tub... -

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Basic information

Entry
Database: PDB / ID: 3cxu
TitleStructure of a Y149F mutant of epoxide hydrolase from Solanum tuberosum
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / EPOXIDE HYDROLASE / ALPHA/BETA HYDROLASE FOLD / Y149F / PROTON WIRE
Function / homology
Function and homology information


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
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNaworyta, A. / Mowbray, S.L. / Widersten, M. / Thomaeus, A.
Citation
Journal: Protein Sci. / Year: 2008
Title: Removal of distal protein-water hydrogen bonds in a plant epoxide hydrolase increases catalytic turnover but decreases thermostability
Authors: Thomaeus, A. / Naworyta, A. / Mowbray, S.L. / Widersten, M.
#1: Journal: Protein Sci. / Year: 2006
Title: X-ray structure of potato epoxide hydrolase sheds light on substrate specificity in plant enzymes
Authors: Mowbray, S.L. / Elfstrom, L.T. / Ahlgren, K.M. / Andersson, C.E. / Widersten, M.
History
DepositionApr 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4733
Polymers74,2792
Non-polymers1941
Water11,782654
1
A: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3342
Polymers37,1401
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,1401
Polymers37,1401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.969, 96.749, 122.215
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Epoxide hydrolase


Mass: 37139.551 Da / Num. of mol.: 2 / Mutation: Y149F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Strain: Lehmi Russet / Plasmid: pGTacStEH1-5H-Y149F / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: Q41415, soluble epoxide hydrolase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG 10000, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2007 / Details: Single Silicon (111) monochromator
RadiationMonochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 45424 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8 / Num. unique all: 27087 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
DNAdata collection
MOLREPphasing
RefinementStarting model: PDB entry 2cjp

2cjp


Resolution: 2→19.976 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.187 / SU B: 3.206 / SU ML: 0.092 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.185 / ESU R Free: 0.152 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 2318 5.109 %random
Rwork0.169 ---
all0.17 ---
obs0.17 45367 99.574 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.144 Å20 Å20 Å2
2---0.057 Å20 Å2
3----0.088 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.152 Å0.185 Å
Luzzati sigma a-0.092 Å
Refinement stepCycle: LAST / Resolution: 2→19.976 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5113 0 13 654 5780
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.03
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0510.2261840.1713085328099.665
2.051-2.1070.2141690.1733016321299.159
2.107-2.1670.2041590.1722939311999.327
2.167-2.2330.2111640.1692887306299.641
2.233-2.3060.2131610.1722756292899.624
2.306-2.3850.2251280.172710284599.754
2.385-2.4740.2071280.1742645277599.928
2.474-2.5730.2451290.182525265999.812
2.573-2.6860.1951310.1772446258199.845
2.686-2.8140.2461270.1882311244099.918
2.814-2.9630.171190.17222492368100
2.963-3.1390.1951230.1712078222798.833
3.139-3.350.215990.1591971207599.759
3.35-3.610.208950.1531863198298.789
3.61-3.9410.197920.1551730182799.726
3.941-4.3850.163890.1541566165799.879
4.385-5.0230.212690.1471425149699.866
5.023-6.0570.194660.191215128399.844
6.057-8.1980.182500.1929961046100
8.198-19.9760.15360.1863669996.137

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