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- PDB-7vx2: Crystal Structure of the Y53F/N55A/I80F/L114V/I116V mutant of LEH -

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Basic information

Entry
Database: PDB / ID: 7vx2
TitleCrystal Structure of the Y53F/N55A/I80F/L114V/I116V 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: 2.485 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 12, 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

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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)69,5648
Polymers69,2424
Non-polymers3224
Water1,04558
1
A: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7454
Polymers34,6212
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-2 kcal/mol
Surface area12280 Å2
MethodPISA
2
B: Limonene-1,2-epoxide hydrolase
C: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8194
Polymers34,6212
Non-polymers1982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-9 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.154, 84.039, 93.371
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 17310.398 Da / Num. of mol.: 4 / Mutation: Y53F, N55A, I80F, L114V, I116V
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
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Ammonium acetate, 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: 1.0331 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: 1.0331 Å / Relative weight: 1
ReflectionResolution: 2.485→50 Å / Num. obs: 20046 / % possible obs: 94.64 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.98 Å2 / CC1/2: 0.994 / CC star: 0.999 / Net I/σ(I): 9.59
Reflection shellResolution: 2.485→2.574 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.35 / Num. unique obs: 1838 / CC1/2: 0.926 / CC star: 0.98 / % possible all: 89.47

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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: 2.485→27.801 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 1039 5.19 %
Rwork0.2312 18977 -
obs0.2336 20016 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.13 Å2 / Biso mean: 29.5623 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 2.485→27.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 51 58 4731
Biso mean--32.92 21.69 -
Num. residues----591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034756
X-RAY DIFFRACTIONf_angle_d0.556455
X-RAY DIFFRACTIONf_chiral_restr0.041717
X-RAY DIFFRACTIONf_plane_restr0.004840
X-RAY DIFFRACTIONf_dihedral_angle_d11.6822822
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.485-2.61540.3421490.2836252590
2.6154-2.77910.33761390.2626266095
2.7791-2.99350.32041520.2764261392
2.9935-3.29430.30961340.266265493
3.2943-3.770.28391700.225270796
3.77-4.74590.21631400.1941287099
4.7459-27.8010.23281550.2013294898

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