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- PDB-4xbx: Crystal Structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V ... -

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Basic information

Entry
Database: PDB / ID: 4xbx
TitleCrystal Structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V mutant of LEH
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase
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
Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
Model detailsA mutant of limonene 1,2-epoxide hydrolase
AuthorsKong, X.D. / Sun, Z. / Xu, J.H. / Reetz, M.T. / Zhou, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Reshaping an Enzyme Binding Pocket for Enhanced and Inverted Stereoselectivity: Use of Smallest Amino Acid Alphabets in Directed Evolution
Authors: Sun, Z. / Lonsdale, R. / Kong, X.D. / Xu, J.H. / Zhou, J. / Reetz, M.T.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: citation / diffrn_detector ...citation / diffrn_detector / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _diffrn_detector.detector ..._citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)69,2374
Polymers69,2374
Non-polymers00
Water20,1591119
1
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)34,6192
Polymers34,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-4 kcal/mol
Surface area12740 Å2
MethodPISA
2
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)34,6192
Polymers34,6192
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-3 kcal/mol
Surface area12880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.756, 91.575, 66.355
Angle α, β, γ (deg.)90.000, 90.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17309.305 Da / Num. of mol.: 4 / Fragment: UNP residues 2-149 / Mutation: L74F/M78F/L103V/L114V/I116V/F139V/L147V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1119 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.4 M citrate sodium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 89376 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.032 / Rrim(I) all: 0.078 / Χ2: 0.997 / Net I/av σ(I): 17.44 / Net I/σ(I): 19.2 / Num. measured all: 494325
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.585.50.14789510.9880.0670.1621.084100
1.58-1.655.50.12689230.990.0570.1381.093100
1.65-1.725.50.1188940.9910.050.1220.976100
1.72-1.815.50.09589360.9930.0420.1041.004100
1.81-1.935.60.08289510.9940.0370.090.987100
1.93-2.085.60.07189410.9960.0320.0780.962100
2.08-2.295.60.06889430.9960.030.0750.99199.9
2.29-2.625.60.07689240.9940.0340.0840.91599.8
2.62-3.35.50.08289710.9930.0370.090.97299.7
3.3-505.40.05289420.9970.0240.0580.98498.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NU3

1nu3


Resolution: 1.53→49.756 Å / FOM work R set: 0.9055 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 4345 4.87 %
Rwork0.147 84943 -
obs0.1483 89288 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.63 Å2 / Biso mean: 13.31 Å2 / Biso min: 2.16 Å2
Refinement stepCycle: final / Resolution: 1.53→49.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4606 0 0 1119 5725
Biso mean---24.79 -
Num. residues----589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064785
X-RAY DIFFRACTIONf_angle_d1.0946543
X-RAY DIFFRACTIONf_chiral_restr0.076743
X-RAY DIFFRACTIONf_plane_restr0.007854
X-RAY DIFFRACTIONf_dihedral_angle_d11.331735
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.53-1.54740.22311570.164528042961100
1.5474-1.56560.1541470.154428412988100
1.5656-1.58470.19941240.153328382962100
1.5847-1.60480.17941400.135128552995100
1.6048-1.62590.18211670.133727972964100
1.6259-1.64810.17661680.137428032971100
1.6481-1.67170.16061430.138428142957100
1.6717-1.69660.19251870.138927962983100
1.6966-1.72320.1511270.145328442971100
1.7232-1.75140.19541290.142228382967100
1.7514-1.78160.14971360.14628312967100
1.7816-1.8140.19691230.141228662989100
1.814-1.84890.16831750.149328112986100
1.8489-1.88660.20721400.158828242964100
1.8866-1.92770.19541420.147328372979100
1.9277-1.97250.18531230.147928352958100
1.9725-2.02180.1631500.146128492999100
2.0218-2.07650.15531440.144928472991100
2.0765-2.13760.19791270.145328422969100
2.1376-2.20660.18091270.146528582985100
2.2066-2.28550.15371290.144728552984100
2.2855-2.3770.20431500.147728302980100
2.377-2.48520.17111460.148928222968100
2.4852-2.61620.17551520.157128212973100
2.6162-2.78010.18371480.160328452993100
2.7801-2.99470.17091350.158728312966100
2.9947-3.2960.20681590.152328402999100
3.296-3.77280.15171360.13492835297199
3.7728-4.75280.14281580.12452828298699
4.7528-49.78210.16441560.16752806296297

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