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- PDB-5yao: The complex structure of SZ529 and expoxid -

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Basic information

Entry
Database: PDB / ID: 5yao
TitleThe complex structure of SZ529 and expoxid
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / epoxide / stereoselective / mutant
Function / homology
Function and homology information


limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity
Similarity search - Function
Limonene-1,2-epoxide hydrolase / Limonene-1,2-epoxide hydrolase catalytic domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
(1R,5S)-6-oxabicyclo[3.1.0]hexane / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.611 Å
AuthorsLian, W. / Sun, Z.T. / Zhou, J.H. / Reetz, M.T.
Funding support China, 2items
OrganizationGrant numberCountry
Strategic Priority Research Program (B) of the Chinese Academy of SciencesXDB20000000 China
Science and Technology Commission of Shanghai Municipality15JC1400403 China
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations
Authors: Sun, Z. / Wu, L. / Bocola, M. / Chan, H.C.S. / Lonsdale, R. / Kong, X.D. / Yuan, S. / Zhou, J. / Reetz, M.T.
History
DepositionSep 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7695
Polymers34,6392
Non-polymers1303
Water43224
1
A: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4263
Polymers17,3191
Non-polymers1072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3422
Polymers17,3191
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.226, 61.097, 120.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Limonene-1,2-epoxide hydrolase


Mass: 17319.320 Da / Num. of mol.: 2 / Fragment: UNP residues 2-149 / Mutation: M32V, M78V, I80V, L114T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical ChemComp-3ZS / (1R,5S)-6-oxabicyclo[3.1.0]hexane


Mass: 84.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8O
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.84 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.4 M sodium citrate, 0.1 M Hepes pH 7.0 / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.93911 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93911 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12436 / % possible obs: 100 % / Redundancy: 7.1 % / Net I/σ(I): 16.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 7 % / Num. unique obs: 608 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CF2

5cf2


Resolution: 2.611→40.133 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2824 634 5.11 %
Rwork0.233 --
obs0.2355 12413 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.611→40.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 8 24 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082120
X-RAY DIFFRACTIONf_angle_d0.9672886
X-RAY DIFFRACTIONf_dihedral_angle_d17.5871260
X-RAY DIFFRACTIONf_chiral_restr0.052326
X-RAY DIFFRACTIONf_plane_restr0.006374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6115-2.8130.33841170.26772225X-RAY DIFFRACTION96
2.813-3.0960.30351330.25932318X-RAY DIFFRACTION100
3.096-3.54380.2911160.24962365X-RAY DIFFRACTION100
3.5438-4.46390.25381190.21072381X-RAY DIFFRACTION100
4.4639-40.13740.27651490.22242490X-RAY DIFFRACTION100

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