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- PDB-5jpu: Structure of limonene epoxide hydrolase mutant - H-2-H5 complex w... -

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Basic information

Entry
Database: PDB / ID: 5jpu
TitleStructure of limonene epoxide hydrolase mutant - H-2-H5 complex with (S,S)-cyclohexane-1,2-diol
Componentslimonene epoxide hydrolase
KeywordsHYDROLASE / Epoxide Hydrolase / Enantioselectivity / 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 / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, G. / Zhang, H. / Sun, Z. / Liu, X. / Reetz, M.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370925 China
CitationJournal: To be published
Title: Multi-Parameter Optimization in Directed Evolution: Engineering Thermostability, Enantioselectivity and Activity of an Epoxide Hydrolase
Authors: Li, G. / Zhang, H. / Sun, Z. / Liu, X. / Reetz, M.T.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _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
A: limonene epoxide hydrolase
B: limonene epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2344
Polymers35,0012
Non-polymers2322
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-12 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.539, 65.539, 72.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein limonene epoxide hydrolase


Mass: 17500.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZAG3*PLUS
#2: Chemical ChemComp-3ZQ / (1S,2S)-cyclohexane-1,2-diol


Mass: 116.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES (pH 7.5), 2% v/v Polyethylene glycol 400, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97916 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 49387 / % possible obs: 100 % / Redundancy: 14.8 % / Net I/σ(I): 35.7
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NU3

1nu3


Resolution: 1.5→24.363 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.94
RfactorNum. reflection% reflection
Rfree0.2463 2496 5.06 %
Rwork0.2279 --
obs0.2288 49334 99.98 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Bsol: 43.377 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 0 241 2129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071930
X-RAY DIFFRACTIONf_angle_d1.1962618
X-RAY DIFFRACTIONf_dihedral_angle_d13.646696
X-RAY DIFFRACTIONf_chiral_restr0.079296
X-RAY DIFFRACTIONf_plane_restr0.006334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4996-1.52840.2611510.22232595X-RAY DIFFRACTION100
1.5284-1.55960.24511260.20932590X-RAY DIFFRACTION100
1.5596-1.59350.22521400.20752612X-RAY DIFFRACTION100
1.5935-1.63060.25141370.21012586X-RAY DIFFRACTION100
1.6306-1.67130.25891330.21152563X-RAY DIFFRACTION100
1.6713-1.71650.23781370.22512613X-RAY DIFFRACTION100
1.7165-1.7670.21661460.21462595X-RAY DIFFRACTION100
1.767-1.8240.23621400.21842576X-RAY DIFFRACTION100
1.824-1.88920.241440.22822587X-RAY DIFFRACTION100
1.8892-1.96480.25761340.22552609X-RAY DIFFRACTION100
1.9648-2.05420.24261510.23522576X-RAY DIFFRACTION100
2.0542-2.16240.22031290.21282602X-RAY DIFFRACTION100
2.1624-2.29780.24551570.21482587X-RAY DIFFRACTION100
2.2978-2.47510.26231200.21782623X-RAY DIFFRACTION100
2.4751-2.72390.25251470.23872627X-RAY DIFFRACTION100
2.7239-3.11730.30891340.25882596X-RAY DIFFRACTION100
3.1173-3.92480.24361440.23072631X-RAY DIFFRACTION100
3.9248-24.3660.21871260.2292670X-RAY DIFFRACTION100

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