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- PDB-5tme: Crystal structure of Os79 from O. sativa in complex with UDP. -

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Basic information

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


quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / detoxification / 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
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 79
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsWetterhorn, K.M. / Newmister, S.A. / Caniza, R.K. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I.
Funding support United States, Austria, 5items
OrganizationGrant numberCountry
National Institute of Food and Agriculture (NIFA, United States)1006542 United States
United States Department of Agriculture (USDA)59-0206-1-117 United States
Department of Energy (DOE, United States)W-31-109-ENG-38 United States
Vienna Science and Technolgy FundLS12-021 Austria
Austrian Science Fund FWFSFB Fusarium Austria
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 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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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)51,5482
Polymers51,1441
Non-polymers4041
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.067, 83.306, 98.249
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
Details: The initial glycine is left over from TEV cleavage
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-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 47.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 50 mM HEPES pH 7.6, 10 mM glycine, 13% MEPEG 5000, 4% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 47323 / % possible obs: 99.9 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 47.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→49.17 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.088 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 2381 5 %RANDOM
Rwork0.18614 ---
obs0.18822 44791 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.141 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.52 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.78→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 25 199 3592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193537
X-RAY DIFFRACTIONr_bond_other_d0.0010.023386
X-RAY DIFFRACTIONr_angle_refined_deg2.0931.9884827
X-RAY DIFFRACTIONr_angle_other_deg0.9693.0017806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4115452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.61922.697152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75615582
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8631535
X-RAY DIFFRACTIONr_chiral_restr0.1250.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02788
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 1.779→1.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 164 -
Rwork0.213 3240 -
obs--98.52 %

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