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- PDB-6bk2: Crystal structure of Os79 H122A/L123A from O. sativa in complex w... -

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Basic information

Entry
Database: PDB / ID: 6bk2
TitleCrystal structure of Os79 H122A/L123A from O. sativa in complex with UDP.
ComponentsUDP-glycosyltransferase 79
KeywordsTRANSFERASE / UDP-glucosyltransferase / trichothecene
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 / Resolution: 1.68 Å
AuthorsWetterhorn, K. / Gabardi, K. / Rayment, I.
CitationJournal: Biochemistry / Year: 2017
Title: Determinants and Expansion of Specificity in a Trichothecene UDP-Glucosyltransferase from Oryza sativa.
Authors: Wetterhorn, K.M. / Gabardi, K. / Michlmayr, H. / Malachova, A. / Busman, M. / McCormick, S.P. / Berthiller, F. / Adam, G. / Rayment, I.
History
DepositionNov 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.3Mar 13, 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: UDP-glycosyltransferase 79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4392
Polymers51,0351
Non-polymers4041
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.552, 83.118, 99.384
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 UDP-glycosyltransferase 79 / OsUGT79 / Deoxynivalenol-UDP-glucosyltransferase


Mass: 51035.055 Da / Num. of mol.: 1 / Mutation: H122A, L123A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice)
Gene: UGT79, OS79, Os04g0206600, LOC_Os04g12970, OsJ_13826, OSJNBa0052O21.15
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 486 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50 mM HEPES pH 7.0, 18% methyl ether polyethylene glycol 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.29→50 Å / Num. obs: 115974 / % possible obs: 99.2 % / Redundancy: 12.3 % / Net I/σ(I): 34.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 1.68→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.445 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18715 2827 5 %RANDOM
Rwork0.15186 ---
obs0.15364 53665 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.974 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 1.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 25 486 3963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0193612
X-RAY DIFFRACTIONr_bond_other_d0.0020.023435
X-RAY DIFFRACTIONr_angle_refined_deg2.4721.9814922
X-RAY DIFFRACTIONr_angle_other_deg1.04737915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50422.739157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415583
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9331535
X-RAY DIFFRACTIONr_chiral_restr0.140.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0214076
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02817
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_it2.2631.661806
X-RAY DIFFRACTIONr_mcbond_other2.2571.6591805
X-RAY DIFFRACTIONr_mcangle_it3.2972.4822260
X-RAY DIFFRACTIONr_mcangle_other3.2972.4832261
X-RAY DIFFRACTIONr_scbond_it3.822.0951806
X-RAY DIFFRACTIONr_scbond_other3.8212.0951805
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7092.9662658
X-RAY DIFFRACTIONr_long_range_B_refined7.53115.5254581
X-RAY DIFFRACTIONr_long_range_B_other7.3714.6314307
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.683→1.727 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 189 -
Rwork0.153 3852 -
obs--97.61 %

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