[English] 日本語
Yorodumi
- PDB-1s9n: Solution structure of the nitrous acid (G)-(G) cross-linked DNA d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1s9n
TitleSolution structure of the nitrous acid (G)-(G) cross-linked DNA dodecamer duplex GCATCC(G)GATGC
Components5'-D(*GP*CP*AP*TP*CP*CP*GP*GP*AP*TP*GP*C)-3'
KeywordsDNA / CROSS-LINK / NITROUS ACID / EXTRAHELICAL CYTOSINES / MINOR GROOVE
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, relaxation matrix
AuthorsEdfeldt, N.B.F. / Harwood, E.A. / Sigurdsson, S.T. / Hopkins, P.B. / Reid, B.R.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Solution structure of a nitrous acid induced DNA interstrand cross-link
Authors: Edfeldt, N.B.F. / Harwood, E.A. / Sigurdsson, S.T. / Hopkins, P.B. / Reid, B.R.
History
DepositionFeb 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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
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_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*CP*AP*TP*CP*CP*GP*GP*AP*TP*GP*C)-3'
B: 5'-D(*GP*CP*AP*TP*CP*CP*GP*GP*AP*TP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)26 / 40back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1

-
Components

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


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Chemically synthesized according to Harwood et al.(1999) J. Am. Chem. Soc. 121, 5081-5082

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131H-P HETCOR
NMR detailsText: This structure was determined using standard 2D homonuclear techniques

-
Sample preparation

DetailsContents: 1mM DNA, 10mM Phosphate pH 7.0, 200mM NaCl, 1mM EDTA
Sample conditionsIonic strength: 200mM / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX5002

-
Processing

SoftwareName: DISCOVER / Version: 1 / Classification: refinement
NMR software
NameVersionDeveloperClassification
XwinNMR1Brukercollection
Felix1Hareprocessing
Felix1Haredata analysis
DGII1Biosymstructure solution
Discover1Biosymstructure solution
BIRDER1Zuiterative matrix relaxation
Discover1Biosymrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, relaxation matrix
Software ordinal: 1
Details: The structures are based on a total of 715 distance restraints (560 are NOE-derived, 52 based on hydrogen bonding, 103 repulsive) and 178 dihedral angle restraints (106 backbone and 72 chiral).
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 40 / Conformers submitted total number: 26

+
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