[English] 日本語
Yorodumi
- PDB-8j2u: Glucosyl Transferase NbUGT72AY1 co-crystallized with UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8j2u
TitleGlucosyl Transferase NbUGT72AY1 co-crystallized with UDP
ComponentsGlycosyltransferase
KeywordsTRANSFERASE / Glucosyl transferase
Function / homologyUDP-glucosyltransferase activity / UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / Transferases; Glycosyltransferases; Hexosyltransferases / URIDINE-5'-DIPHOSPHATE / Glycosyltransferase
Function and homology information
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Glucosyl Transferase NbUGT72AY1 co-crystallized with UDP
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyltransferase
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,7004
Polymers107,8922
Non-polymers8082
Water0
1
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3502
Polymers53,9461
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-8 kcal/mol
Surface area19630 Å2
MethodPISA
2
B: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3502
Polymers53,9461
Non-polymers4041
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.492, 112.559, 103.632
Angle α, β, γ (deg.)90.00, 102.25, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Glycosyltransferase /


Mass: 53945.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nicotiana tabacum (common tobacco) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8K1ZRH3
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium chloride, 0.1 M MES pH 6.0, 20% w/vPEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 3.32→45.96 Å / Num. obs: 16627 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.96 / Net I/σ(I): 3
Reflection shellResolution: 3.32→3.41 Å / Num. unique obs: 1133 / CC1/2: 0.37

-
Processing

Software
NameVersionClassification
REFMACRefmac5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.32→45.96 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.842 / SU B: 54.784 / SU ML: 0.759 / Cross valid method: THROUGHOUT / ESU R Free: 0.79 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.33038 1040 6.3 %RANDOM
Rwork0.28937 ---
obs0.29196 15354 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 114.807 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.27 Å2
2--0.35 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 3.32→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 50 0 7510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0177658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0167240
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.84410404
X-RAY DIFFRACTIONr_angle_other_deg0.3661.5616926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3875.193982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.433101406
X-RAY DIFFRACTIONr_chiral_restr0.0470.21226
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028412
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021364
X-RAY DIFFRACTIONr_mcbond_it2.12511.8093782
X-RAY DIFFRACTIONr_mcbond_other2.12511.8093782
X-RAY DIFFRACTIONr_mcangle_it3.70217.74724
X-RAY DIFFRACTIONr_mcangle_other3.70217.7014725
X-RAY DIFFRACTIONr_scbond_it1.63711.8553876
X-RAY DIFFRACTIONr_scbond_other1.58811.8433869
X-RAY DIFFRACTIONr_scangle_other3.04917.7655681
X-RAY DIFFRACTIONr_long_range_B_refined9.82333344
X-RAY DIFFRACTIONr_long_range_B_other9.82433345
LS refinement shellResolution: 3.32→3.405 Å
RfactorNum. reflection% reflection
Rfree0.492 68 -
Rwork0.47 1059 -
obs--91.48 %

+
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