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- PDB-1nu3: Limonene-1,2-epoxide hydrolase in complex with valpromide -

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Basic information

Entry
Database: PDB / ID: 1nu3
TitleLimonene-1,2-epoxide hydrolase in complex with valpromide
Componentslimonene-1,2-epoxide hydrolase
KeywordsHYDROLASE / PROTEIN-LIGAND 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
2-PROPYLPENTANAMIDE / Limonene-1,2-epoxide hydrolase
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsArand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L.
CitationJournal: EMBO J. / Year: 2003
Title: Structure of Rhodococcus erythropolis limonene-1,2-epoxide hydrolase reveals a novel active site
Authors: Arand, M. / Hallberg, B.M. / Zou, J. / Bergfors, T. / Oesch, F. / van der Werf, M.J. / de Bont, J.A.M. / Jones, T.A. / Mowbray, S.L.
History
DepositionJan 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)33,8665
Polymers33,3842
Non-polymers4823
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint14 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.596, 47.656, 129.244
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 16692.131 Da / Num. of mol.: 2 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Plasmid: pGEF-LEH / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 34.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 6000, LiCl, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112.8 mg/mlprotein1drop
210 mMHEPES1droppH7.0
330 %PEG60001reservoir
41 M1reservoirLiCl
50.1 MMES1reservoirpH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.944 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 18, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.944 Å / Relative weight: 1
ReflectionResolution: 1.75→29 Å / Num. all: 29009 / Num. obs: 29009 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 3.9 % / Rsym value: 0.056 / Net I/σ(I): 20.7
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 12.2 / Rsym value: 0.107 / % possible all: 97.5
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 97.5 % / Rmerge(I) obs: 0.107

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→29 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.961 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19533 1469 5.1 %RANDOM
Rwork0.15759 ---
all0.15945 27715 --
obs0.15945 27485 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.13 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.051 Å
Refinement stepCycle: LAST / Resolution: 1.75→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2281 0 32 330 2643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222359
X-RAY DIFFRACTIONr_bond_other_d0.0020.022140
X-RAY DIFFRACTIONr_angle_refined_deg1.9211.9763199
X-RAY DIFFRACTIONr_angle_other_deg0.85534975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1825290
X-RAY DIFFRACTIONr_chiral_restr0.1120.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022624
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02474
X-RAY DIFFRACTIONr_nbd_refined0.1970.2424
X-RAY DIFFRACTIONr_nbd_other0.2480.22516
X-RAY DIFFRACTIONr_nbtor_other0.0840.21400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2215
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2780.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.223
X-RAY DIFFRACTIONr_mcbond_it0.9321.51458
X-RAY DIFFRACTIONr_mcangle_it1.54122342
X-RAY DIFFRACTIONr_scbond_it2.533901
X-RAY DIFFRACTIONr_scangle_it4.0684.5857
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.227 118
Rwork0.172 1902
Refinement
*PLUS
Lowest resolution: 29 Å / Rfactor Rfree: 0.195 / Rfactor Rwork: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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