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

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Basic information

Entry
Database: PDB / ID: 4xbt
TitleCrystal Structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V mutant of LEH complexed with (S,S)-cyclohexanediol
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase / product complex
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
(1S,2S)-cyclohexane-1,2-diol / CITRATE ANION / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
Model detailsA mutant of limonene 1,2-epoxide hydrolase
AuthorsKong, X.D. / Sun, Z. / Lonsdale, R. / 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _software.name

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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)69,8488
Polymers69,2374
Non-polymers6114
Water16,051891
1
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9244
Polymers34,6192
Non-polymers3052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-4 kcal/mol
Surface area12450 Å2
MethodPISA
2
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9244
Polymers34,6192
Non-polymers3052
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-5 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.743, 66.455, 91.549
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A & B and chains C & D)

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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: Chemical ChemComp-3ZQ / (1S,2S)-cyclohexane-1,2-diol


Mass: 116.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 891 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 64002 / % possible obs: 97.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 20.55 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.039 / Rrim(I) all: 0.084 / Χ2: 1.013 / Net I/av σ(I): 18.228 / Net I/σ(I): 12.1 / Num. measured all: 285740
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.764.40.55762290.8030.2920.6310.99295.5
1.76-1.834.40.41862990.8850.2190.4741.05896
1.83-1.914.40.30663030.9230.1610.3471.04696.5
1.91-2.024.40.20863620.9630.110.2360.98496.8
2.02-2.144.40.14763800.9790.0780.1670.94797.6
2.14-2.314.40.12364530.9840.0650.140.98998.2
2.31-2.544.50.10164770.9880.0530.1151.03198.8
2.54-2.914.60.07865520.9930.040.0881.0199.2
2.91-3.664.50.05462520.9960.0280.0611.08494.5
3.66-504.60.0466950.9980.020.0450.98999.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1nu3


Resolution: 1.7→33.681 Å / FOM work R set: 0.876 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1954 3250 5.08 %gel filtration
Rwork0.1564 60715 --
obs0.1584 63965 97.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.74 Å2 / Biso mean: 21.72 Å2 / Biso min: 10.52 Å2
Refinement stepCycle: final / Resolution: 1.7→33.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4597 0 42 891 5530
Biso mean--30.64 30.39 -
Num. residues----587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064802
X-RAY DIFFRACTIONf_angle_d1.2146560
X-RAY DIFFRACTIONf_chiral_restr0.075743
X-RAY DIFFRACTIONf_plane_restr0.007854
X-RAY DIFFRACTIONf_dihedral_angle_d13.3271764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72540.29881170.23932595271295
1.7254-1.75240.2591570.20832554271195
1.7524-1.78110.24611270.19152581270896
1.7811-1.81180.22771330.17672595272896
1.8118-1.84470.20871280.18422656278496
1.8447-1.88020.24341370.19432564270197
1.8802-1.91860.23951420.17712630277297
1.9186-1.96030.19771440.16312598274297
1.9603-2.00590.20041330.16172619275297
2.0059-2.05610.21831510.15472656280798
2.0561-2.11160.25361490.15952592274198
2.1116-2.17380.18811320.15682700283298
2.1738-2.24390.21391390.16332639277898
2.2439-2.32410.19021410.15532641278298
2.3241-2.41710.19881370.15722693283099
2.4171-2.52710.20261360.16232704284099
2.5271-2.66030.22241510.15822669282099
2.6603-2.82690.18931480.163727082856100
2.8269-3.0450.20651510.159726852836100
3.045-3.35120.17811530.158427362889100
3.3512-3.83550.17721260.13722394252088
3.8355-4.83010.15041480.120827332881100
4.8301-33.68740.18111700.15892773294399

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