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- PDB-5tmd: Crystal structure of Os79 from O. sativa in complex with U2F and ... -

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Basic information

Entry
Database: PDB / ID: 5tmd
TitleCrystal structure of Os79 from O. sativa in complex with U2F and trichothecene.
ComponentsGlycosyltransferase, Os79
KeywordsTRANSFERASE / mycotoxin / UDP-glucosyltransferase / trichothecene / detoxification
Function / homology
Function and homology information


detoxification / quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding / cytoplasm
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trichothecene / Chem-U2F / UDP-glycosyltransferase 79
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsWetterhorn, K. / Newmister, S.A. / Caniza, R.K. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I.
CitationJournal: Biochemistry / Year: 2016
Title: Crystal Structure of Os79 (Os04g0206600) from Oryza sativa: A UDP-glucosyltransferase Involved in the Detoxification of Deoxynivalenol.
Authors: Wetterhorn, K.M. / Newmister, S.A. / Caniza, R.K. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I.
History
DepositionOct 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Glycosyltransferase, Os79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9473
Polymers51,1441
Non-polymers8032
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.441, 83.155, 99.425
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 Glycosyltransferase, Os79


Mass: 51144.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: Os04g0206600, Os04g0206600, OSJNBa0052O21.15, OSNPB_040206600
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q7XT97, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#3: Chemical ChemComp-7E0 / trichothecene / (11beta)-12,13-epoxytrichothec-9-ene


Mass: 234.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES pH 6.5, 200 mM glycine, 23% MEPEG 2000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.19→43.5 Å / Num. obs: 25837 / % possible obs: 99.6 % / Redundancy: 7.8 % / Net I/σ(I): 19.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PHENIXrefinement
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→43.5 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.438 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.186 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21335 1317 5.1 %RANDOM
Rwork0.15958 ---
obs0.16242 24520 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.19→43.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 53 261 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193546
X-RAY DIFFRACTIONr_bond_other_d0.0020.023366
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.9934831
X-RAY DIFFRACTIONr_angle_other_deg0.96937761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3255438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.94722.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65615568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7021532
X-RAY DIFFRACTIONr_chiral_restr0.120.2537
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02784
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_it2.7143.0651758
X-RAY DIFFRACTIONr_mcbond_other2.7123.0641757
X-RAY DIFFRACTIONr_mcangle_it3.9034.5842194
X-RAY DIFFRACTIONr_mcangle_other3.9024.5852195
X-RAY DIFFRACTIONr_scbond_it3.9623.5941788
X-RAY DIFFRACTIONr_scbond_other3.9613.5941788
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.985.2192635
X-RAY DIFFRACTIONr_long_range_B_refined8.18326.0754290
X-RAY DIFFRACTIONr_long_range_B_other8.16625.7994181
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.192→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 73 -
Rwork0.172 1690 -
obs--94.43 %

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