[English] 日本語
Yorodumi
- PDB-7msn: SunS glycosin S-glycosyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7msn
TitleSunS glycosin S-glycosyltransferase
ComponentsSPbeta prophage-derived glycosyltransferase SunS
KeywordsTRANSFERASE / glycosin / RiPP / S-glycosyltransferase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


: / bacteriocin biosynthetic process / UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity
Similarity search - Function
Peptide S-glycosyltransferase, SunS family / Glycosyltransferase 2-like / Glycosyl transferase family 2 / Nucleotide-diphospho-sugar transferases / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE-GLUCOSE / SPbeta prophage-derived glycosyltransferase SunS
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGarg, N. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Cell Chem Biol / Year: 2021
Title: Structural and mechanistic investigations of protein S-glycosyltransferases.
Authors: Fujinami, D. / Garcia de Gonzalo, C.V. / Biswas, S. / Hao, Y. / Wang, H. / Garg, N. / Lukk, T. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SPbeta prophage-derived glycosyltransferase SunS
B: SPbeta prophage-derived glycosyltransferase SunS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7944
Polymers99,6612
Non-polymers1,1332
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-59 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.730, 108.730, 210.697
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein SPbeta prophage-derived glycosyltransferase SunS


Mass: 49830.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: sunS, yolJ, BSU21450 / Production host: Escherichia coli (E. coli)
References: UniProt: O31986, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 50 mM HEPES, pH=7.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 47618 / % possible obs: 91.2 % / Redundancy: 7.4 % / CC1/2: 0.998 / Net I/σ(I): 20.1
Reflection shellResolution: 3→3.1 Å / Num. unique obs: 2476 / CC1/2: 0.8

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.38 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 30.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 2438 5.12 %
Rwork0.2041 45180 -
obs0.2079 47618 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.74 Å2 / Biso mean: 64.9662 Å2 / Biso min: 22.1 Å2
Refinement stepCycle: final / Resolution: 3→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6923 0 72 0 6995
Biso mean--62.14 --
Num. residues----833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.060.40731340.33682534266895
3.06-3.130.33731280.31232647277599
3.13-3.20.36871580.303827132871100
3.2-3.280.3241700.277526192789100
3.28-3.370.42031360.271926832819100
3.37-3.470.33051620.2562660282299
3.47-3.580.39711570.25092666282399
3.58-3.710.32721240.244126842808100
3.71-3.860.35561260.22432699282599
3.86-4.030.28821490.18642681283099
4.03-4.250.21111450.18032655280099
4.25-4.510.23191500.16022674282499
4.51-4.860.22921520.1592650280299
4.86-5.350.23031490.17112646279599
5.35-6.120.27741540.19862650280499
6.12-7.710.31371210.1992684280599
7.71-47.380.18431230.15272635275897

+
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