[English] 日本語
Yorodumi
- PDB-226d: SOLUTION CONFORMATION OF A BIZELESIN A-TRACT DUPLEX ADDUCT, NMR, ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 226d
TitleSOLUTION CONFORMATION OF A BIZELESIN A-TRACT DUPLEX ADDUCT, NMR, 1 STRUCTURE
Components
  • DNA (5'-D(*CP*GP*TP*AP*AP*AP*AP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*AP*CP*G)-3')
KeywordsDNA / DNA-LIGAND / ADDUCT / BIZELESIN
Function / homologyBIZELESIN / DNA
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR MECHANICS, MOLECULAR DYNAMICS
AuthorsThompson, A.S. / Hurley, L.H.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution conformation of a bizelesin A-tract duplex adduct: DNA-DNA cross-linking of an A-tract straightens out bent DNA.
Authors: Thompson, A.S. / Hurley, L.H.
History
DepositionJul 19, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*AP*AP*AP*AP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8353
Polymers6,0882
Non-polymers7471
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: DNA chain DNA (5'-D(*CP*GP*TP*TP*TP*TP*TP*AP*CP*G)-3')


Mass: 3025.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*CP*GP*TP*AP*AP*AP*AP*AP*CP*G)-3')


Mass: 3062.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Chemical ChemComp-BIZ / BIZELESIN / 6,6'-{CARBONYLBIS(IMINO-1H-INDOLE-5,2-DIYLCARBONYL)}BIS{8-(CHLOROMETHYL)-3,6,7,8-TETRAHYDRO-1-METHYL-BENZO{1,2-B,4,3-B'}DIPYRROL-4-OL{S-(R*,R*)} / BIZELESIN


Mass: 746.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H38N8O5 / Details: CHEMICALLY SYNTHESIZED / Comment: antibiotic*YM

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

SoftwareName: AMBER / Classification: refinement
NMR software
NameVersionClassification
Amber4refinement
MARDIGRASrefinement
RefinementMethod: RESTRAINED MOLECULAR MECHANICS, MOLECULAR DYNAMICS / Software ordinal: 1
Details: THE STRUCTURE WAS REFINED USING A COMBINATION OF RESTRAINED MOLECULAR MECHANICS AND DYNAMICS USING THE AMBER 4.0 PROGRAM (UCSF). DISTANCE RESTRAINTS WERE CALCULATED USING MARDIGRAS FROM ...Details: THE STRUCTURE WAS REFINED USING A COMBINATION OF RESTRAINED MOLECULAR MECHANICS AND DYNAMICS USING THE AMBER 4.0 PROGRAM (UCSF). DISTANCE RESTRAINTS WERE CALCULATED USING MARDIGRAS FROM NUCLEAR OVERHAUSER EFFECT SPECTRA AT VARIOUS MIXING TIMES.
NMR ensembleConformers submitted total number: 1

+
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