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- PDB-4inz: The crystal structure of M145A mutant of an epoxide hydrolase fro... -

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Basic information

Entry
Database: PDB / ID: 4inz
TitleThe crystal structure of M145A mutant of an epoxide hydrolase from Bacillus megaterium
ComponentsSoluble epoxide hydrolase
KeywordsHYDROLASE / a/b hydrolase fold / enzymatic resolution
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
DI(HYDROXYETHYL)ETHER / Soluble epoxide hydrolase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,7275
Polymers70,4532
Non-polymers2743
Water7,098394
1
A: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3953
Polymers35,2271
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3332
Polymers35,2271
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.829, 77.651, 120.034
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 Soluble epoxide hydrolase


Mass: 35226.551 Da / Num. of mol.: 2 / Mutation: M145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Strain: ECU1001 isolate / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3
References: UniProt: G9BEX6, pyrimidine-5'-nucleotide nucleosidase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 34% PEG 3000, 0.2M Lithium sulfate , pH 8.0, 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 14, 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: 1.7→50 Å / Num. obs: 416525 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 16.092
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.7-1.766.40.439199.1
1.76-1.836.50.299199.3
1.83-1.916.50.209199.5
1.91-2.026.40.165199.6
2.02-2.146.50.124199.7
2.14-2.316.50.1199.6
2.31-2.546.60.083199.5
2.54-2.916.70.07199.5
2.91-3.666.30.059197.6
3.66-505.40.05188.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.7_637)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→36.941 Å / SU ML: 0.24 / σ(F): 0 / Phase error: 18.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 3246 5.07 %5
Rwork0.1575 ---
obs0.1602 64070 96.57 %-
all-65111 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.741 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2144 Å20 Å2-0 Å2
2--3.8926 Å20 Å2
3----2.6783 Å2
Refinement stepCycle: LAST / Resolution: 1.7→36.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4711 0 18 394 5123
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054893
X-RAY DIFFRACTIONf_angle_d0.9396640
X-RAY DIFFRACTIONf_dihedral_angle_d13.3511815
X-RAY DIFFRACTIONf_chiral_restr0.071681
X-RAY DIFFRACTIONf_plane_restr0.004871
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.72540.38081280.2929250792
1.7254-1.75230.32521260.2666251594
1.7523-1.78110.2891290.2461258695
1.7811-1.81180.28391260.2155263497
1.8118-1.84470.25321530.1848260797
1.8447-1.88020.2561370.1696262797
1.8802-1.91860.25011540.1368259797
1.9186-1.96030.22651380.1307265098
1.9603-2.00590.19391560.123267498
2.0059-2.05610.19831300.1204268499
2.0561-2.11160.23781650.1209264698
2.1116-2.17380.18171270.1264271099
2.1738-2.24390.20131310.1201268699
2.2439-2.32410.1921760.1216265899
2.3241-2.41710.19471390.1313271199
2.4171-2.52710.22161280.1396272599
2.5271-2.66030.21191530.1394273999
2.6603-2.8270.2061380.1559271299
2.827-3.04510.2111530.1676272999
3.0451-3.35140.21541210.1673274599
3.3514-3.83590.19611560.1577258894
3.8359-4.83110.17441400.1561239185
4.8311-36.94980.20551420.1997270391

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