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- PDB-5yng: Crystal structure of SZ348 in complex with cyclopentene oxide -

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Basic information

Entry
Database: PDB / ID: 5yng
TitleCrystal structure of SZ348 in complex with cyclopentene oxide
ComponentsLimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase / cyclopentene oxide
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,5S)-6-oxabicyclo[3.1.0]hexane / : / NICKEL (II) ION / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.497 Å
AuthorsWu, L. / Sun, Z.T. / Reetz, M.T. / Zhou, J.H.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Structural and Computational Insight into the Catalytic Mechanism of Limonene Epoxide Hydrolase Mutants in Stereoselective Transformations.
Authors: Sun, Z. / Wu, L. / Bocola, M. / Chan, H.C.S. / Lonsdale, R. / Kong, X.D. / Yuan, S. / Zhou, J. / Reetz, M.T.
History
DepositionOct 24, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Limonene-1,2-epoxide hydrolase
B: Limonene-1,2-epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1358
Polymers34,7712
Non-polymers3646
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, one single peak
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-16 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.159, 104.159, 73.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

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


Mass: 17385.424 Da / Num. of mol.: 2 / Mutation: I80Y, L114V, I116V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-3ZS / (1R,5S)-6-oxabicyclo[3.1.0]hexane


Mass: 84.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.32 Å3/Da / Density % sol: 62.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2.4M Na/K phosphate, 3% xylitol, 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.542 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15393 / % possible obs: 96.7 % / Redundancy: 6.7 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.497→38.459 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 749 4.87 %
Rwork0.1899 --
obs0.1924 15390 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.497→38.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2361 0 16 47 2424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082450
X-RAY DIFFRACTIONf_angle_d0.9373335
X-RAY DIFFRACTIONf_dihedral_angle_d13.1781457
X-RAY DIFFRACTIONf_chiral_restr0.05371
X-RAY DIFFRACTIONf_plane_restr0.007431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.497-2.68970.33531360.28042874X-RAY DIFFRACTION95
2.6897-2.96030.33251830.26042853X-RAY DIFFRACTION96
2.9603-3.38840.29311420.21512937X-RAY DIFFRACTION97
3.3884-4.26820.20111530.16112931X-RAY DIFFRACTION97
4.2682-38.4640.19991350.16173046X-RAY DIFFRACTION98

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