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- PDB-6bk1: Crystal structure of Os79 T291V from O. sativa in complex with UDP. -

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Basic information

Entry
Database: PDB / ID: 6bk1
TitleCrystal structure of Os79 T291V 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 / MOLECULAR REPLACEMENT / Resolution: 1.58 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 1.3Oct 4, 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: UDP-glycosyltransferase 79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5462
Polymers51,1421
Non-polymers4041
Water8,917495
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.462, 83.219, 98.670
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: 51142.234 Da / Num. of mol.: 1 / Mutation: T291V
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


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


Mass: 18.015 Da / Num. of mol.: 495 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 50 mM HEPES pH 7.5, 32% MEPEG 5K

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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 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 63979 / % possible obs: 99.8 % / Redundancy: 8.4 % / Net I/σ(I): 83.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tme

5tme


Resolution: 1.58→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.254 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.078 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 3395 5 %RANDOM
Rwork0.16457 ---
obs0.16617 63979 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.877 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 25 495 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0193514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023340
X-RAY DIFFRACTIONr_angle_refined_deg2.5041.9824778
X-RAY DIFFRACTIONr_angle_other_deg1.12337696
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1995438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48322.961152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4515568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2351532
X-RAY DIFFRACTIONr_chiral_restr0.1750.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
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_it2.4752.4471758
X-RAY DIFFRACTIONr_mcbond_other2.4692.4461757
X-RAY DIFFRACTIONr_mcangle_it3.3813.6662194
X-RAY DIFFRACTIONr_mcangle_other3.3823.6662195
X-RAY DIFFRACTIONr_scbond_it4.3452.8651756
X-RAY DIFFRACTIONr_scbond_other4.2932.8641755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9384.142585
X-RAY DIFFRACTIONr_long_range_B_refined7.24822.0554445
X-RAY DIFFRACTIONr_long_range_B_other7.25722.064446
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 266 -
Rwork0.178 4629 -
obs--98.93 %

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