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- PDB-5aig: Discovery and characterization of thermophilic limonene-1,2-epoxi... -

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Basic information

Entry
Database: PDB / ID: 5aig
TitleDiscovery and characterization of thermophilic limonene-1,2-epoxide hydrolases from hot spring metagenomic libraries. Tomsk-sample- Valpromide complex
ComponentsLIMONENE-1,2-EPOXIDE HYDROLASE
KeywordsHYDROLASE
Function / homologyNuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / 2-PROPYLPENTANAMIDE
Function and homology information
Biological speciesUNIDENTIFIED (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 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 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Jan 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7958
Polymers28,1962
Non-polymers5996
Water8,845491
1
A: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3974
Polymers14,0981
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LIMONENE-1,2-EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3974
Polymers14,0981
Non-polymers2993
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)96.460, 96.460, 56.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.20842, 0.97797, 0.01206), (0.97791, -0.20857, 0.01366), (0.01588, 0.00895, -0.99983)
Vector: -0.33533, 0.13449, 21.13291)

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Components

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


Mass: 14097.941 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-VPR / 2-PROPYLPENTANAMIDE / VALPROMIDE


Mass: 143.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H17NO
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENBANK KP765711

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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: 2.71 Å3/Da / Density % sol: 55.7 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.16→48.2 Å / Num. obs: 104136 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 9.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 1.16→1.19 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NWW

1nww


Resolution: 1.16→48.23 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.02 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.13265 5139 4.9 %RANDOM
Rwork0.108 ---
obs0.10923 98956 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.935 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å20 Å2
2---0.45 Å20 Å2
3---1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.16→48.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 36 491 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022512
X-RAY DIFFRACTIONr_bond_other_d0.0040.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.621.9423491
X-RAY DIFFRACTIONr_angle_other_deg1.86135616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8165357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27923.566143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.06915452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4981528
X-RAY DIFFRACTIONr_chiral_restr0.1130.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023002
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02658
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_it2.4423.6721126
X-RAY DIFFRACTIONr_mcbond_other2.473.6471125
X-RAY DIFFRACTIONr_mcangle_it3.386.2141440
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6094.7361386
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_restr3.97634933
X-RAY DIFFRACTIONr_sphericity_free40.232525
X-RAY DIFFRACTIONr_sphericity_bonded17.18955289
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 397 -
Rwork0.228 7237 -
obs--99.49 %

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