[English] 日本語
Yorodumi
- PDB-1bgu: CRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSF... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bgu
TitleCRYSTAL STRUCTURE OF THE DNA MODIFYING ENZYME BETA-GLUCOSYLTRANSFERASE IN THE PRESENCE AND ABSENCE OF THE SUBSTRATE URIDINE DIPHOSPHOGLUCOSE
ComponentsBETA-GLUCOSYLTRANSFERASE
KeywordsTRANSFERASE(GLUCOSYLTRANSFERASE)
Function / homologyDNA beta-glucosyltransferase / DNA beta-glucosyltransferase activity / DNA beta-glucosyltransferase, bacteriophage / Bacteriophage T4 beta-glucosyltransferase / symbiont-mediated evasion of host restriction-modification system / DNA modification / virus-mediated perturbation of host defense response / URIDINE-5'-DIPHOSPHATE / DNA beta-glucosyltransferase
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsVrielink, A. / Rueger, W. / Driessen, H.P.C. / Freemont, P.S.
Citation
Journal: EMBO J. / Year: 1994
Title: Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
Authors: Vrielink, A. / Ruger, W. / Driessen, H.P. / Freemont, P.S.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization and Preliminary X-Ray Studies of T4 Phage Beta-Glucosyltransferase
Authors: Freemont, P.S. / Rueger, W.
#2: Journal: Nucleic Acids Res. / Year: 1985
Title: T4-Induced Alpha-and Beta-Glucosyltransferase: Cloning of the Genes and a Comparison of Their Products Based on Sequencing Data
Authors: Tomaschewski, J. / Gram, H. / Crabb, J.W. / Ruger, W.
History
DepositionJun 9, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-GLUCOSYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1242
Polymers40,7201
Non-polymers4041
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.920, 52.260, 52.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein BETA-GLUCOSYLTRANSFERASE / Coordinate model: Cα atoms only


Mass: 40719.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / References: UniProt: P04547, DNA beta-glucosyltransferase
#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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal grow
*PLUS
Method: unknown
Details: This particular structure is not described in this paper.

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0
Details: THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS TRANSLATED BY 1/4*151.920 ALONG A AND 1/4*52.26 ALONG B. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE ...Details: THE COORDINATES ARE PRESENTED IN A COORDINATE FRAME THAT IS TRANSLATED BY 1/4*151.920 ALONG A AND 1/4*52.26 ALONG B. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE DEFAULT. THE DICTIONARY FOR THE UDP PORTION OF THE SUBSTRATE WAS BUILT USING THE CHARM MINIMIZATION WITHIN QUANTA.
RfactorNum. reflection
Rwork0.191 -
obs0.191 20885
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms328 0 25 0 353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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://pdbjlvh1.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