[English] 日本語
Yorodumi
- PDB-1i7v: THE SOLUTION STRUCTURE OF A BAY REGION 1R-BENZ[A]ANTHRACENE OXIDE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i7v
TitleTHE SOLUTION STRUCTURE OF A BAY REGION 1R-BENZ[A]ANTHRACENE OXIDE ADDUCT AT THE N6 POSITION OF ADENINE OF AN OLIGODEOXYNUCLEOTIDE CONTAINING THE HUMAN N-RAS CODON 61 SEQUENCE
Components
  • 5'-D(*CP*GP*GP*AP*CP*AP*(BZA)AP*GP*AP*AP*G)-3'
  • 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'
KeywordsDNA / Benz[a]anthracene-DNA duplex
Function / homologyChem-BZA / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / NOE-restrained molecular dynamics, simulated annealing
AuthorsLi, Z. / Tamura, P.J. / Wilkinson, A.S. / Harris, C.M. / Harris, T.M. / Stone, M.P.
CitationJournal: Biochemistry / Year: 2001
Title: Intercalation of the (1R,2S,3R,4S)-N6-[1-(1,2,3,4-tetrahydro-2,3,4-trihydroxybenz[a]anthracenyl)]-2'-deoxyadenosyl adduct in the N-ras codon 61 sequence: DNA sequence effects
Authors: Li, Z. / Tamura, P.J. / Wilkinson, A.S. / Harris, C.M. / Harris, T.M. / Stone, M.P.
History
DepositionMar 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,9883
Polymers6,7072
Non-polymers2801
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 / 1back calculated data agree with experimental NOESY spectrum
Representative

-
Components

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


Mass: 3416.263 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3'


Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-BZA / 1R,2S,3R,4S-TETRAHYDRO-BENZO[A]ANTHRACENE-2,3,4-TRIOL


Mass: 280.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16O3

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
2222D NOESY
232DQF-COSY
242TOCSY
NMR detailsText: This structure was determined using 2D homonuclear techniques

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.8 mM oligodeoxynucleotide, 10 mM phosphate buffer, 0.05 mM EDTA, 0.1 M NaCl90% H2O/10% D2O
21.8 mM oligodeoxynucleotide, 10 mM phosphate buffer, 0.05 mM EDTA, 0.1 M NaCl100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.1 M NaCl 7.0 1 atm278 K
20.1 M NaCl 7.0 1 atm288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX7502

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
X-PLOR3.851A. Brungerstructure solution
Felix97Biosym Technologiesprocessing
CORMA5.2Borgias, B.A., Thomas, P.D., Li, H., Kumar, A., and Tonelli, M.refinement
MARDIGRAS3Borgias, B.A., Thomas, P.D., Li, H., Kumar, A., and Tonelli, M.iterative matrix relaxation
RefinementMethod: NOE-restrained molecular dynamics, simulated annealing
Software ordinal: 1
Details: The structure was based on a total of 485 NOE derived distance constraints.
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 1 / Conformers 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://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