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- PDB-5cxo: Intriguing role of epoxide hydrolase/cyclase-like enzyme SalBIII ... -

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Basic information

Entry
Database: PDB / ID: 5cxo
TitleIntriguing role of epoxide hydrolase/cyclase-like enzyme SalBIII in pyran ring formation in polyether salinomycin
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / salinomycin polyether cyclase / epoxide hydrolase
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / hydrolase activity / Roll / Alpha Beta / Epoxide hydrolase
Function and homology information
Biological speciesStreptomyces albus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDias, M.V.B. / Luhavaya, H. / Williams, S.R. / Hong, H. / Oliveira, L.G. / Leadlay, P.F.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2010/15971-3 Brazil
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Enzymology of Pyran Ring A Formation in Salinomycin Biosynthesis.
Authors: Luhavaya, H. / Dias, M.V. / Williams, S.R. / Hong, H. / de Oliveira, L.G. / Leadlay, P.F.
History
DepositionJul 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4597
Polymers33,0472
Non-polymers1,4125
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-8 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.047, 101.935, 120.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-310-

HOH

21B-368-

HOH

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Components

#1: Protein Epoxide hydrolase / Putative epoxide hydrolase


Mass: 16523.424 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces albus (bacteria) / Gene: slnBI, SLNWT_0271 / Plasmid: pET29a / Details (production host): C-terminal His tag / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: H6D578
#2: Chemical
ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% PEG 400, 20% PEG3350, 0.1 M MgCl2, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9772373 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772373 Å / Relative weight: 1
ReflectionResolution: 1.8→77.92 Å / Num. obs: 30391 / % possible obs: 98.9 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 37
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 6.8 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rga

3rga


Resolution: 1.8→77.92 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.544 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27517 1539 5.1 %RANDOM
Rwork0.2109 ---
obs0.21415 28849 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.432 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2---0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→77.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 65 163 2272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022139
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3361.9592869
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1885263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.13725104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6415363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9181516
X-RAY DIFFRACTIONr_chiral_restr0.1640.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0211586
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_it4.2673.5021052
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.3285.2181312
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0574.0591087
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.57331.1293383
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 109 -
Rwork0.331 2106 -
obs--97.97 %

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