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- PDB-5i10: Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase sp... -

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Basic information

Entry
Database: PDB / ID: 5i10
TitleCrystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa
ComponentsProbable O-methyltransferase
KeywordsTRANSFERASE
Function / homologyMacrocin-O-methyltransferase (TylF) / Macrocin-O-methyltransferase / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / metal ion binding / O-methyltransferase/macrocin O-methyltransferase/8-demethyl-8-(2, 3-dimethoxy-alpha-L-rhamnosyl)tetracenomycin-C 4'-O-methyltransferase
Function and homology information
Biological speciesSaccharopolyspora spinosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, Y.-C. / Huang, S.-P. / Huang, B.-L. / Chen, Y.-H. / Chen, Y.-J. / Chiu, H.-T.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science CouncilNSC102-2113-M006-003-MY2 Taiwan
CitationJournal: To Be Published
Title: Crystal structure of spinosyn rhamnosyl 4'-O-methyltransferase spnh mutant T242Q from Saccharopolyspora Spinosa
Authors: Lin, Y.-C. / Huang, S.-P. / Huang, B.-L. / Chen, Y.-H. / Chen, Y.-J. / Chiu, H.-T.
History
DepositionFeb 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Assembly

Deposited unit
A: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1332
Polymers28,1091
Non-polymers241
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-8 kcal/mol
Surface area8930 Å2
MethodPISA
2
A: Probable O-methyltransferase
hetero molecules

A: Probable O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2664
Polymers56,2172
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_566x,x-y+1,-z+7/61
Buried area1730 Å2
ΔGint-28 kcal/mol
Surface area16330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.776, 54.776, 306.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

21A-482-

HOH

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Components

#1: Protein Probable O-methyltransferase


Mass: 28108.504 Da / Num. of mol.: 1 / Mutation: T242Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora spinosa (bacteria) / Gene: spnH / Plasmid: PET-21B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9ALM9
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 18-24% (w/v) polyethylene glycol 3350, 100mM Tris, pH 7-9, 200mM magnesium chloride and 2.3mM SRPG
PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 28, 2015 / Details: RH COATED MIRROWS
RadiationMonochromator: LN2-COOLED, FIXED-EXIT DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→27.6 Å / Num. obs: 26486 / % possible obs: 99.45 % / Observed criterion σ(I): 1 / Redundancy: 38.4 % / Biso Wilson estimate: 34.2 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 39.04
Reflection shellResolution: 2.06→2.15 Å / Redundancy: 35.6 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 3.23 / % possible all: 94.52

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CDZ

4cdz


Resolution: 2→27.6 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 30.31
RfactorNum. reflection% reflection
Rfree0.2637 1396 7.54 %
Rwork0.2269 --
obs0.2297 18526 94.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 46.1 Å2
Refinement stepCycle: LAST / Resolution: 2→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 1 97 1622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051560
X-RAY DIFFRACTIONf_angle_d0.9332119
X-RAY DIFFRACTIONf_dihedral_angle_d13.666558
X-RAY DIFFRACTIONf_chiral_restr0.034233
X-RAY DIFFRACTIONf_plane_restr0.003273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07150.431270.34761528X-RAY DIFFRACTION87
2.0715-2.15440.36351300.30241647X-RAY DIFFRACTION94
2.1544-2.25240.48421130.39641439X-RAY DIFFRACTION82
2.2524-2.37110.48521210.35881468X-RAY DIFFRACTION82
2.3711-2.51960.30111440.26611723X-RAY DIFFRACTION98
2.5196-2.7140.27151460.24891797X-RAY DIFFRACTION100
2.714-2.98680.27371470.24711786X-RAY DIFFRACTION99
2.9868-3.41830.28041500.23931844X-RAY DIFFRACTION100
3.4183-4.30410.22341530.19211862X-RAY DIFFRACTION100
4.3041-27.66920.21021650.18362036X-RAY DIFFRACTION100

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