[English] 日本語
Yorodumi
- PDB-8wvd: Crystal structure of Glycosyltransferase in complex with UD1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8wvd
TitleCrystal structure of Glycosyltransferase in complex with UD1
ComponentsGlycosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


mogroside IE synthase / quercetin 3-O-glucosyltransferase activity / quercetin 7-O-glucosyltransferase activity / UDP-glucosyltransferase activity
Similarity search - Function
UDP-glycosyltransferase family, conserved site / UDP-glycosyltransferases signature. / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Mogroside I-E synthase
Similarity search - Component
Biological speciesSiraitia grosvenorii (arhat fruit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsLi, J. / Shan, N. / Yang, J.G. / Liu, W.D. / Sun, Y.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2024
Title: Enzymatic Synthesis of Novel Terpenoid Glycoside Derivatives Decorated with N -Acetylglucosamine Catalyzed by UGT74AC1.
Authors: Li, J. / Li, R. / Shang, N. / Men, Y. / Cai, Y. / Zeng, Y. / Liu, W. / Yang, J. / Sun, Y.
History
DepositionOct 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8292
Polymers51,2211
Non-polymers6071
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-6 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.867, 68.825, 142.689
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Glycosyltransferase / ugt transferase


Mass: 51221.477 Da / Num. of mol.: 1 / Mutation: H18A,D111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Siraitia grosvenorii (arhat fruit) / Gene: UDPG1 / Production host: Escherichia coli (E. coli)
References: UniProt: K7NBW3, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: PEG8000, MgAC

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→25 Å / Num. obs: 57492 / % possible obs: 98.7 % / Redundancy: 17.4 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.2
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.635 / Num. unique obs: 5021 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQ6

2pq6


Resolution: 1.66→24.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.969 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.107
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2869 5 %RANDOM
Rwork0.19 ---
obs0.192 54545 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.56 Å2 / Biso mean: 32.79 Å2 / Biso min: 15.02 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2---2.99 Å20 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 1.66→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3569 0 64 337 3970
Biso mean--20 40.44 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133695
X-RAY DIFFRACTIONr_bond_other_d00.0173420
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.645022
X-RAY DIFFRACTIONr_angle_other_deg1.2411.5737984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0275449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98223.657175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.9615648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9171515
X-RAY DIFFRACTIONr_chiral_restr0.0710.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.020.024032
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02725
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.66→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 163 -
Rwork0.311 3207 -
all-3370 -
obs--79.88 %

+
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