[English] 日本語
Yorodumi
- PDB-6bk0: Crystal structure of Os79 Q202A from O. sativa in complex with UDP. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6bk0
TitleCrystal structure of Os79 Q202A from O. sativa in complex with UDP.
ComponentsUDP-glycosyltransferase 79
KeywordsTRANSFERASE / UDP-glucosyltransferase / trichothecene
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
URIDINE-5'-DIPHOSPHATE / UDP-glycosyltransferase 79
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 79
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4912
Polymers51,0871
Non-polymers4041
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.409, 83.233, 99.098
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein UDP-glycosyltransferase 79 / OsUGT79 / Deoxynivalenol-UDP-glucosyltransferase


Mass: 51087.156 Da / Num. of mol.: 1 / Mutation: Q202A
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-Gold(DE3)pLysS AG
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.: 583 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM 3-(N- Morpholino)propanesulfonic acid pH 7.5, 15% methyl ether polyethylene glycol 5000 (MEPEG 5K), 160 mM potassium glutamate

-
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: Dec 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 79234 / % possible obs: 99.2 % / Redundancy: 13.1 % / Net I/σ(I): 41.3

-
Processing

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

5tme


Resolution: 1.47→43.46 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 0.863 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18068 4150 5 %RANDOM
Rwork0.15267 ---
obs0.15408 79234 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.157 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.47→43.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 25 583 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0410.0193574
X-RAY DIFFRACTIONr_bond_other_d0.0020.023414
X-RAY DIFFRACTIONr_angle_refined_deg2.8741.9834869
X-RAY DIFFRACTIONr_angle_other_deg1.11937867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.07622.727154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52915580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.461534
X-RAY DIFFRACTIONr_chiral_restr0.1710.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
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_it2.1111.5981781
X-RAY DIFFRACTIONr_mcbond_other2.1051.5971780
X-RAY DIFFRACTIONr_mcangle_it3.1222.3852224
X-RAY DIFFRACTIONr_mcangle_other3.1242.3862225
X-RAY DIFFRACTIONr_scbond_it3.5541.9311793
X-RAY DIFFRACTIONr_scbond_other3.5551.9311792
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1442.7682640
X-RAY DIFFRACTIONr_long_range_B_refined7.08715.1884632
X-RAY DIFFRACTIONr_long_range_B_other6.84614.0354286
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 287 -
Rwork0.165 5764 -
obs--98.57 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more