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- PDB-4xdv: Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH compl... -

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Basic information

Entry
Database: PDB / ID: 4xdv
TitleCrystal Structure of the L74F/M78V/I80V/L114F mutant of LEH complexed with cyclohexanediol
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
(1R,2R)-cyclohexane-1,2-diol / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Limonene-1,2-epoxide hydrolase
E: Limonene-1,2-epoxide hydrolase
G: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
F: Limonene-1,2-epoxide hydrolase
H: Limonene-1,2-epoxide hydrolase
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,42012
Polymers138,9558
Non-polymers4654
Water12,178676
1
C: Limonene-1,2-epoxide hydrolase
D: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9714
Polymers34,7392
Non-polymers2322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-12 kcal/mol
Surface area12370 Å2
MethodPISA
2
E: Limonene-1,2-epoxide hydrolase
F: Limonene-1,2-epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)34,7392
Polymers34,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-12 kcal/mol
Surface area12360 Å2
MethodPISA
3
G: Limonene-1,2-epoxide hydrolase
H: Limonene-1,2-epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)34,7392
Polymers34,7392
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-12 kcal/mol
Surface area12450 Å2
MethodPISA
4
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9714
Polymers34,7392
Non-polymers2322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-13 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.699, 61.161, 119.552
Angle α, β, γ (deg.)90.000, 90.150, 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: 17369.381 Da / Num. of mol.: 8 / Fragment: UNP residues 5-149 / Mutation: L74F/M78V/I80V/L114F
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-40O / (1R,2R)-cyclohexane-1,2-diol


Mass: 116.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 676 / 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: 2.97 Å3/Da / Density % sol: 58.59 %
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: Oct 25, 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: 2.25→50 Å / Num. obs: 70793 / % possible obs: 97.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 41.26 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.055 / Rrim(I) all: 0.127 / Χ2: 1.001 / Net I/av σ(I): 10.503 / Net I/σ(I): 11.6 / Num. measured all: 376437
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.335.10.70369870.7620.3380.7831.12697.2
2.33-2.425.40.4970100.870.2280.5421.02397.8
2.42-2.535.40.39771120.9310.1850.4390.97598.5
2.53-2.675.30.371340.9530.140.3320.98898.8
2.67-2.835.40.2471570.9610.1120.2660.9699.1
2.83-3.055.50.17971710.9770.0840.1990.97499.1
3.05-3.365.40.13472120.9850.0630.1490.99699.4
3.36-3.8550.10669130.990.0520.1190.98995.3
3.85-4.855.20.08568100.990.0420.0951.00493.2
4.85-505.50.05772870.9960.0270.0640.98197.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→33.524 Å / FOM work R set: 0.7422 / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.97 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2815 3503 4.95 %
Rwork0.2212 67195 -
obs0.2242 70698 96.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.18 Å2 / Biso mean: 33.96 Å2 / Biso min: 8.91 Å2
Refinement stepCycle: final / Resolution: 2.25→33.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8839 0 30 676 9545
Biso mean--30.44 31.5 -
Num. residues----1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089098
X-RAY DIFFRACTIONf_angle_d1.0912369
X-RAY DIFFRACTIONf_chiral_restr0.0681373
X-RAY DIFFRACTIONf_plane_restr0.0061613
X-RAY DIFFRACTIONf_dihedral_angle_d16.0713254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2406-2.27130.41531190.40052020213973
2.2713-2.30380.36641440.31592638278297
2.3038-2.33810.30741400.26162739287998
2.3381-2.37470.28491460.24892695284198
2.3747-2.41360.3221510.24342661281298
2.4136-2.45520.28511240.25262731285598
2.4552-2.49980.3621200.26662733285399
2.4998-2.54790.35851690.24772750291999
2.5479-2.59990.31661070.23742727283499
2.5999-2.65640.34281480.23812751289999
2.6564-2.71810.36071590.24552683284299
2.7181-2.78610.34121380.24022792293099
2.7861-2.86140.34011490.24572709285899
2.8614-2.94550.31321390.24482781292099
2.9455-3.04050.32691350.23412779291499
3.0405-3.14910.28071390.2272725286499
3.1491-3.27510.28071780.22742764294299
3.2751-3.4240.30421400.22082705284599
3.424-3.60440.28981470.22272690283796
3.6044-3.82990.24741480.21062575272393
3.8299-4.12510.2271200.2042603272393
4.1251-4.53930.25261330.18762643277694
4.5393-5.19410.22361330.17712670280394
5.1941-6.53610.23711330.20428262959100
6.5361-33.52820.25691440.2132805294996

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