[English] 日本語
Yorodumi
- PDB-8xfh: Crystal structure of MiCGT(E152Q/V190D/S122P) in complex with UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xfh
TitleCrystal structure of MiCGT(E152Q/V190D/S122P) in complex with UDP
ComponentsUDP-glycosyltransferase 13
KeywordsTRANSFERASE
Function / homology
Function and homology information


xylosyltransferase activity / UDP-glucosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases
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-5'-DIPHOSPHATE / UDP-glycosyltransferase 13
Similarity search - Component
Biological speciesMangifera indica (mango)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.80000300155 Å
AuthorsZhang, Z.M. / Zhou, Z.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: An efficient C-glycoside production platform enabled by rationally tuning the chemoselectivity of glycosyltransferases.
Authors: Li, M. / Zhou, Y. / Wen, Z. / Ni, Q. / Zhou, Z. / Liu, Y. / Zhou, Q. / Jia, Z. / Guo, B. / Ma, Y. / Chen, B. / Zhang, Z.M. / Wang, J.B.
History
DepositionDec 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 9, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glycosyltransferase 13
B: UDP-glycosyltransferase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6404
Polymers102,8322
Non-polymers8082
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-9 kcal/mol
Surface area18340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.532, 103.354, 108.966
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

#1: Protein UDP-glycosyltransferase 13


Mass: 51415.922 Da / Num. of mol.: 2 / Mutation: S122P, E152Q, V190D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mangifera indica (mango) / Gene: CGT / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0M4KE44
#2: Chemical ChemComp-UDP / URIDINE-5'-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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200mM calcium acetate,100mM tris (PH 6.5-7.5),PEG 3000 16%-22%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.8→47.15 Å / Num. obs: 26288 / % possible obs: 99.32 % / Redundancy: 12.8 % / Biso Wilson estimate: 58.6869915508 Å2 / CC1/2: 0.969 / Net I/σ(I): 2.1
Reflection shellResolution: 2.902→3.005 Å / Num. unique obs: 6917 / CC1/2: 0.969

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.80000300155→37.4939106389 Å / SU ML: 0.358095563705 / Cross valid method: FREE R-VALUE / σ(F): 1.35397126728 / Phase error: 25.4054548227
RfactorNum. reflection% reflection
Rfree0.244109439651 1979 7.52814972611 %
Rwork0.221176572174 24309 -
obs0.222902956102 26288 99.7344259807 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.0269374521 Å2
Refinement stepCycle: LAST / Resolution: 2.80000300155→37.4939106389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6644 0 50 0 6694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003202067430266868
X-RAY DIFFRACTIONf_angle_d0.8342708289619397
X-RAY DIFFRACTIONf_chiral_restr0.02758198866011082
X-RAY DIFFRACTIONf_plane_restr0.004268754905181206
X-RAY DIFFRACTIONf_dihedral_angle_d15.79373716042387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.870.3188456101291360.3000349966041699X-RAY DIFFRACTION99.9455337691
2.87-2.94760.3264801840081330.2860914529831725X-RAY DIFFRACTION99.8387963461
2.9476-3.03430.3355326345531470.2859669911071690X-RAY DIFFRACTION99.8369565217
3.0343-3.13220.2986740314151350.2781324174011713X-RAY DIFFRACTION99.9459167117
3.1322-3.2440.2997909720661440.2807149478981716X-RAY DIFFRACTION100
3.244-3.37380.2716224759641300.2466585708881709X-RAY DIFFRACTION99.8913633895
3.3738-3.52730.2591687589331370.2419235426031750X-RAY DIFFRACTION99.9470338983
3.5273-3.71310.2594889864741430.233146937521728X-RAY DIFFRACTION100
3.7131-3.94550.2338189573951410.2093958299651724X-RAY DIFFRACTION99.9464094319
3.9455-4.24980.2369934478971450.1940947633551742X-RAY DIFFRACTION99.9470338983
4.2498-4.67670.1888518836671470.1928929631671743X-RAY DIFFRACTION99.8942917548
4.6767-5.35180.2193558269371410.2015150322671761X-RAY DIFFRACTION99.8949579832
5.3518-6.73630.2441918660851430.216968613751779X-RAY DIFFRACTION99.896049896
6.7363-37.490.2131519546811570.1902705752331830X-RAY DIFFRACTION97.5454099165

+
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