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- PDB-4io0: Crystal structure of F128A mutant of an epoxide hydrolase from Ba... -

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Basic information

Entry
Database: PDB / ID: 4io0
TitleCrystal structure of F128A mutant of an epoxide hydrolase from Bacillus megaterium complexed with its product (R)-3-[1]naphthyloxy-propane-1,2-diol
ComponentsSoluble epoxide hydrolase
KeywordsHYDROLASE / a/b hydrolase fold / epoxide hydrolase
Function / homology
Function and homology information


pyrimidine-5'-nucleotide nucleosidase activity / pyrimidine-5'-nucleotide nucleosidase
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
(2R)-3-(naphthalen-1-yloxy)propane-1,2-diol / Soluble epoxide hydrolase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.9 Å
AuthorsKong, X.D. / Zhou, J.H. / Xu, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Engineering of an epoxide hydrolase for efficient bioresolution of bulky pharmaco substrates.
Authors: Kong, X.D. / Yuan, S. / Li, L. / Chen, S. / Xu, J.H. / Zhou, J.H.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Soluble epoxide hydrolase
B: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,0506
Polymers70,4212
Non-polymers6294
Water1,802100
1
A: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5253
Polymers35,2111
Non-polymers3142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5253
Polymers35,2111
Non-polymers3142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.640, 109.640, 117.496
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Soluble epoxide hydrolase


Mass: 35210.574 Da / Num. of mol.: 2 / Mutation: F128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ECU1001 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)
References: UniProt: G9BEX6, pyrimidine-5'-nucleotide nucleosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-RN1 / (2R)-3-(naphthalen-1-yloxy)propane-1,2-diol


Mass: 218.248 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H14O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.51 Å3/Da / Density % sol: 50.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Tris, 2.0 M (NH4)2SO4, 0.2 M Li2SO4, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2012 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 121961 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Rmerge(I) obs: 0.221 / Rsym value: 0.221 / Net I/σ(I): 8.337
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.9-37.40.791100
3-3.127.50.5961100
3.12-3.277.50.4781100
3.27-3.447.50.3751100
3.44-3.657.50.2731100
3.65-3.947.50.2141100
3.94-4.337.50.1661100
4.33-4.967.40.1391100
4.96-6.247.30.1691100
6.24-506.80.09199.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_637)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD
Starting model: 4G00

4g00
PDB Unreleased entry


Resolution: 2.9→45.25 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 804 5.06 %5
Rwork0.156 ---
obs0.1598 15898 96.68 %-
all-16484 --
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.973 Å2 / ksol: 0.342 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3344 Å20 Å20 Å2
2---0.3344 Å2-0 Å2
3---0.6688 Å2
Refinement stepCycle: LAST / Resolution: 2.9→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 42 100 4861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084912
X-RAY DIFFRACTIONf_angle_d1.1176666
X-RAY DIFFRACTIONf_dihedral_angle_d16.3651810
X-RAY DIFFRACTIONf_chiral_restr0.075681
X-RAY DIFFRACTIONf_plane_restr0.004870
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9002-3.08180.32051540.2171230792
3.0818-3.31970.29861290.2022244295
3.3197-3.65370.25811310.1606248997
3.6537-4.1820.19391320.1235252498
4.182-5.26760.17851360.1165258099
5.2676-45.25590.21741220.1733275299

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