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- PDB-4nzz: Crystal structure of epoxide hydrolase from bacillus megaterium -

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Basic information

Entry
Database: PDB / ID: 4nzz
TitleCrystal structure of epoxide hydrolase from bacillus megaterium
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
Soluble epoxide hydrolase
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 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.
History
DepositionDec 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)74,1772
Polymers74,1772
Non-polymers00
Water7,458414
1
A: Soluble epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,0891
Polymers37,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Soluble epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,0891
Polymers37,0891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.231, 76.006, 120.808
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: 37088.668 Da / Num. of mol.: 2
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
References: UniProt: G9BEX6, pyrimidine-5'-nucleotide nucleosidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 0.5M LICL, 0.1M TRIS-HCL, 28% PEG 6000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, EVAPORATION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 26, 2010
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.749→64.333 Å / Num. obs: 59760 / % possible obs: 99 % / Observed criterion σ(I): 2
Reflection shellResolution: 1.75→1.81 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(PHENIX.REFINE: 1.7_637)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.75→35.58 Å / SU ML: 0.22 / σ(F): 0 / Phase error: 23.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2918 5.05 %
Rwork0.186 --
obs0.188 57830 95.8 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.57 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.2599 Å20 Å2-0 Å2
2--9.258 Å20 Å2
3----5.998 Å2
Refinement stepCycle: LAST / Resolution: 1.75→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4748 0 0 414 5162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075006
X-RAY DIFFRACTIONf_angle_d0.9956804
X-RAY DIFFRACTIONf_dihedral_angle_d14.3551862
X-RAY DIFFRACTIONf_chiral_restr0.075693
X-RAY DIFFRACTIONf_plane_restr0.004901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77870.38741110.32742112X-RAY DIFFRACTION77
1.7787-1.80940.37161320.30512201X-RAY DIFFRACTION84
1.8094-1.84230.38551260.26742388X-RAY DIFFRACTION88
1.8423-1.87770.31321160.24172470X-RAY DIFFRACTION91
1.8777-1.91610.27531400.22072488X-RAY DIFFRACTION93
1.9161-1.95770.24071480.22342587X-RAY DIFFRACTION95
1.9577-2.00330.26421400.22542567X-RAY DIFFRACTION96
2.0033-2.05340.27771300.22442618X-RAY DIFFRACTION97
2.0534-2.10890.26031330.21342655X-RAY DIFFRACTION97
2.1089-2.17090.28731430.2052666X-RAY DIFFRACTION98
2.1709-2.2410.25391480.20732661X-RAY DIFFRACTION99
2.241-2.3210.2711270.20312705X-RAY DIFFRACTION99
2.321-2.4140.25121360.20292692X-RAY DIFFRACTION99
2.414-2.52380.26541470.19862727X-RAY DIFFRACTION99
2.5238-2.65680.22851630.19722682X-RAY DIFFRACTION100
2.6568-2.82320.25291670.19892715X-RAY DIFFRACTION100
2.8232-3.04110.24711560.20162747X-RAY DIFFRACTION100
3.0411-3.34690.22571470.19892738X-RAY DIFFRACTION100
3.3469-3.83070.2181410.16532775X-RAY DIFFRACTION100
3.8307-4.82440.15971380.13442804X-RAY DIFFRACTION100
4.8244-35.59090.18961290.15152914X-RAY DIFFRACTION98

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