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- PDB-7xef: Crystal Structure of the Y53F/N55A mutant of LEH complexed with (... -

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Basic information

Entry
Database: PDB / ID: 7xef
TitleCrystal Structure of the Y53F/N55A mutant of LEH complexed with (R)-(1-benzyl-3-phenylpyrrolidin-3-yl)methanol
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 / Chem-D0I / DI(HYDROXYETHYL)ETHER / Limonene-1,2-epoxide hydrolase
Function and homology information
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.816 Å
AuthorsQu, G. / Li, X. / Sun, Z.T.
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
DepositionMar 31, 2022Deposition 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)70,96622
Polymers69,2184
Non-polymers1,74818
Water12,629701
1
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3379
Polymers34,6092
Non-polymers7287
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-3 kcal/mol
Surface area12920 Å2
MethodPISA
2
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,62913
Polymers34,6092
Non-polymers1,02011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-2 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.862, 51.024, 65.077
Angle α, β, γ (deg.)69.890, 79.160, 63.810
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, 719 molecules

#2: Chemical
ChemComp-D0I / [(3~{R})-3-phenyl-1-(phenylmethyl)pyrrolidin-3-yl]methanol


Mass: 267.365 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H21NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.92 %
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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.816→43.7 Å / Num. obs: 45725 / % possible obs: 93.76 % / Redundancy: 3.7 % / Biso Wilson estimate: 12.13 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.23
Reflection shellResolution: 1.816→1.881 Å / Num. unique obs: 4212 / CC1/2: 0.94

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Processing

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

1nww


Resolution: 1.816→43.7 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 19.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 2302 5.03 %
Rwork0.1411 43418 -
obs0.1436 45720 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.93 Å2 / Biso mean: 14.633 Å2 / Biso min: 2.05 Å2
Refinement stepCycle: final / Resolution: 1.816→43.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4674 0 121 701 5496
Biso mean--24.32 23.1 -
Num. residues----598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124966
X-RAY DIFFRACTIONf_angle_d1.1026746
X-RAY DIFFRACTIONf_chiral_restr0.068742
X-RAY DIFFRACTIONf_plane_restr0.008871
X-RAY DIFFRACTIONf_dihedral_angle_d8.1244269
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.816-1.85510.2321120.1451241782
1.8551-1.89820.22761330.1416265991
1.8982-1.94570.22191160.1496264191
1.9457-1.99830.20991560.1537265092
1.9983-2.05710.2161590.1423264792
2.0571-2.12350.21611470.1453267993
2.1235-2.19940.19541450.1395267493
2.1994-2.28750.20781500.1427271694
2.2875-2.39160.20791740.153270594
2.3916-2.51760.25981360.153277395
2.5176-2.67540.21321210.1554278795
2.6754-2.88190.21011620.1484273596
2.8819-3.17180.1561480.1474280497
3.1718-3.63060.17181630.1355279497
3.6306-4.57340.13291420.1157286698
4.5734-43.70.15581380.1354287199

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