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- PDB-7vwd: Crystal Structure of the Y53F/N55A mutant of LEH -

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Basic information

Entry
Database: PDB / ID: 7vwd
TitleCrystal Structure of the Y53F/N55A mutant of LEH
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / limonene-1 / 2-epoxide hydrolase / mutant / Rhodococcus erythropolis
Function / homologylimonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity / Limonene-1,2-epoxide hydrolase / Limonene-1,2-epoxide hydrolase catalytic domain / NTF2-like domain superfamily / DI(HYDROXYETHYL)ETHER / Limonene-1,2-epoxide hydrolase
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 Å
AuthorsQu, G. / Li, X. / Sun, Z.T. / Han, X. / Liu, W.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles.
Authors: Li, J.K. / Qu, G. / Li, X. / Tian, Y. / Cui, C. / Zhang, F.G. / Zhang, W. / Ma, J.A. / Reetz, M.T. / Sun, Z.
History
DepositionNov 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,74714
Polymers69,2184
Non-polymers52910
Water3,225179
1
A: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9157
Polymers34,6092
Non-polymers3065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-1 kcal/mol
Surface area12130 Å2
MethodPISA
2
B: Limonene-1,2-epoxide hydrolase
C: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8327
Polymers34,6092
Non-polymers2235
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-2 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.271, 50.391, 64.729
Angle α, β, γ (deg.)69.820, 79.870, 63.890
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 17304.434 Da / Num. of mol.: 4 / Mutation: Y53F, N55A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase

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Non-polymers , 5 types, 189 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.05 Å3/Da / Density % sol: 40.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: NaCl, BIS-TRIS pH5.5, Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1.033 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 26435 / % possible obs: 93.06 % / Redundancy: 4 % / Biso Wilson estimate: 20.55 Å2 / CC1/2: 0.989 / CC star: 0.997 / Net I/σ(I): 10.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 4 % / Num. unique obs: 2620 / CC1/2: 0.952 / CC star: 0.988 / % possible all: 92.58

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nww

1nww


Resolution: 2.153→26 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 10.5 / Phase error: 22.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2181 1249 4.73 %
Rwork0.1833 25177 -
obs0.185 26426 93.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.64 Å2 / Biso mean: 20.3558 Å2 / Biso min: 10.09 Å2
Refinement stepCycle: final / Resolution: 2.153→26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4594 0 32 179 4805
Biso mean--26.44 20.2 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024728
X-RAY DIFFRACTIONf_angle_d0.4786412
X-RAY DIFFRACTIONf_chiral_restr0.041716
X-RAY DIFFRACTIONf_plane_restr0.004831
X-RAY DIFFRACTIONf_dihedral_angle_d4.1253067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1531-2.23920.23031260.1963281193
2.2392-2.34110.25731470.1952281395
2.3411-2.46440.22531190.2063287195
2.4644-2.61870.29011490.2112281293
2.6187-2.82070.25991270.2116278192
2.8207-3.10410.28191230.2102260886
3.1041-3.55230.2361170.1918291496
3.5523-4.47180.17871740.1504283496
4.4718-260.16911670.1532273392

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