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Basic information

Entry
Database: PDB / ID: 5aii
TitleDiscovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. CH55-sample-PEG complex
ComponentsLIMONENE-1,2-EPOXIDE HYDROLASE
KeywordsHYDROLASE
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HISTIDINE / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Chem-PG6 / TRIETHYLENE GLYCOL
Similarity search - Component
Biological speciesUNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsFerrandi, E. / Sayer, C. / Isupov, M.N. / Annovazzi, C. / Marchesi, C. / Iacobone, G. / Peng, X. / Bonch-Osmolovskaya, E. / Wohlgemuth, R. / Littlechild, J.A. / Montia, D.
CitationJournal: FEBS J. / Year: 2015
Title: Discovery and Characterization of Thermophilic Limonene-1,2-Epoxide Hydrolases from Hot Spring Metagenomic Libraries
Authors: Ferrandi, E.E. / Sayer, C. / Isupov, M.N. / Annovazzi, C. / Marchesi, C. / Iacobone, G. / Peng, X. / Bonch-Osmolovskaya, E. / Wohlgemuth, R. / Littlechild, J.A. / Montia, D.
History
DepositionFeb 13, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
E: LIMONENE-1,2-EPOXIDE HYDROLASE
F: LIMONENE-1,2-EPOXIDE HYDROLASE
G: LIMONENE-1,2-EPOXIDE HYDROLASE
H: LIMONENE-1,2-EPOXIDE HYDROLASE
I: LIMONENE-1,2-EPOXIDE HYDROLASE
J: LIMONENE-1,2-EPOXIDE HYDROLASE
K: LIMONENE-1,2-EPOXIDE HYDROLASE
L: LIMONENE-1,2-EPOXIDE HYDROLASE
M: LIMONENE-1,2-EPOXIDE HYDROLASE
N: LIMONENE-1,2-EPOXIDE HYDROLASE
O: LIMONENE-1,2-EPOXIDE HYDROLASE
P: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,18896
Polymers234,23216
Non-polymers9,95680
Water32,9671830
1
G: LIMONENE-1,2-EPOXIDE HYDROLASE
H: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,52513
Polymers29,2792
Non-polymers1,24611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-4.1 kcal/mol
Surface area12320 Å2
MethodPISA
2
E: LIMONENE-1,2-EPOXIDE HYDROLASE
F: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2929
Polymers29,2792
Non-polymers1,0137
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint5.2 kcal/mol
Surface area11140 Å2
MethodPISA
3
K: LIMONENE-1,2-EPOXIDE HYDROLASE
L: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,42212
Polymers29,2792
Non-polymers1,14310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint2.5 kcal/mol
Surface area11550 Å2
MethodPISA
4
A: LIMONENE-1,2-EPOXIDE HYDROLASE
B: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,47911
Polymers29,2792
Non-polymers1,2009
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-7.6 kcal/mol
Surface area11740 Å2
MethodPISA
5
O: LIMONENE-1,2-EPOXIDE HYDROLASE
P: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,44313
Polymers29,2792
Non-polymers1,16411
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint2.7 kcal/mol
Surface area11920 Å2
MethodPISA
6
C: LIMONENE-1,2-EPOXIDE HYDROLASE
D: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,89116
Polymers29,2792
Non-polymers1,61214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint14 kcal/mol
Surface area11420 Å2
MethodPISA
7
M: LIMONENE-1,2-EPOXIDE HYDROLASE
N: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,73613
Polymers29,2792
Non-polymers1,45711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint4.2 kcal/mol
Surface area13270 Å2
MethodPISA
8
I: LIMONENE-1,2-EPOXIDE HYDROLASE
J: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3999
Polymers29,2792
Non-polymers1,1207
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint10.7 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 104.230, 148.000
Angle α, β, γ (deg.)90.00, 102.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.995, 0.037, 0.095), (0.028, -0.796, 0.605), (0.098, 0.604, 0.791)-25.34749, -26.89003, 10.4838
2given(-0.995, 0.037, 0.095), (0.028, -0.796, 0.605), (0.098, 0.604, 0.791)-25.34749, -26.89003, 10.4838
3given(0.998, 0.057, -0.031), (-0.058, 0.998, -0.01), (0.03, 0.012, 0.999)-16.38792, -0.83746, -70.99185
4given(-0.994, -0.032, 0.105), (0.09, -0.784, 0.614), (0.063, 0.62, 0.782)-43.60597, -27.22577, -60.83347
5given(0.997, -0.009, -0.078), (0.012, 0.999, 0.037), (0.078, -0.038, 0.996)-29.39355, -2.24842, 1.69702
6given(-0.99983, -0.01228, 0.01372), (0.01819, -0.7733, 0.63378), (0.00282, 0.63392, 0.77339)-0.7563, -0.27989, 0.07486
7given(0.892, -0.128, -0.434), (-0.167, 0.799, -0.578), (0.421, 0.588, 0.691)-6.51241, 13.15004, -16.66798
8given(-0.935, -0.135, -0.329), (0.137, -0.99, 0.017), (-0.328, -0.029, 0.944)-30.51628, -10.25231, -36.0321
9given(0.91, -0.14, -0.39), (-0.122, 0.809, -0.575), (0.396, 0.571, 0.719)42.67937, 14.6146, -90.98987
10given(-0.947, -0.092, -0.308), (0.084, -0.996, 0.039), (-0.31, 0.011, 0.951)19.38064, -10.74198, -108.93488
11given(0.882, -0.221, -0.417), (-0.085, 0.796, -0.599), (0.464, 0.564, 0.683)8.13233, 15.9502, -88.41555
12given(-0.92, -0.045, -0.39), (0.051, -0.999, -0.005), (-0.389, -0.025, 0.921)-12.16069, -9.29703, -108.25758
13given(-0.912, -0.073, -0.404), (0.071, -0.997, 0.02), (-0.404, -0.011, 0.915)6.29559, -10.11428, -36.69394
14given(0.857, -0.226, -0.464), (-0.107, 0.802, -0.588), (0.505, 0.553, 0.663)27.692, 15.35975, -15.59412
15given(-0.997, -0.069, 0.021), (0.068, -0.812, 0.58), (-0.023, 0.58, 0.814)-3.39372, -24.97018, -63.59216
16given(0.99, 0.041, -0.133), (-0.046, 0.998, -0.038), (0.131, 0.043, 0.99)24.62529, 1.57717, -69.93742

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Components

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Protein , 1 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
LIMONENE-1,2-EPOXIDE HYDROLASE


Mass: 14639.479 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) UNIDENTIFIED (others) / Plasmid: PRHAM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): 10G / References: limonene-1,2-epoxide hydrolase

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Non-polymers , 9 types, 1910 molecules

#2: Chemical...
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2
#9: Chemical ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE


Mass: 266.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O6
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1830 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGENBANK KP765710

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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: 2.35 Å3/Da / Density % sol: 47.19 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.47→104.2 Å / Num. obs: 336972 / % possible obs: 97.5 % / Observed criterion σ(I): 1.9 / Redundancy: 3.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NWW

1nww


Resolution: 1.47→104.23 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.476 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 16691 5 %RANDOM
Rwork0.17523 ---
obs0.17687 320246 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.644 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å20.66 Å2
2---0.43 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.47→104.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15204 0 663 1830 17697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01917417
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.97723745
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79252359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83322.429774
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.317152725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.24115189
X-RAY DIFFRACTIONr_chiral_restr0.1050.22762
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02113137
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8796.4578440
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.06910.84310595
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9587.3938977
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 1297 -
Rwork0.284 22663 -
obs--94.1 %

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