[English] 日本語
Yorodumi
- PDB-1n4b: Solution Structure of the undecamer CGAAAC*TTTCG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1n4b
TitleSolution Structure of the undecamer CGAAAC*TTTCG
Components
  • 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'
  • 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'
KeywordsDNA / interstrand cross-link / alkylated DNA / modified cytosine / alkylated cytosine
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / distance geometry simulated annealing, molecular dynamics
AuthorsWebba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P.
CitationJournal: Biochemistry / Year: 2002
Title: Solution Structure of a DNA Duplex Containing Mispair-Aligned N4C-Ethyl-N4C Interstrand Cross-Linked Cytosines
Authors: Webba da Silva, M. / Noronha, A.M. / Noll, D.M. / Miller, P.S. / Colvin, O.M. / Gamcsik, M.P.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 2014Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'


Theoretical massNumber of molelcules
Total (without water)6,6942
Polymers6,6942
Non-polymers00
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 / 100the structure submitted is the lowest energy structure of a an ensemble of selected ten structures
RepresentativeModel #1closest to the average,lowest energy

-
Components

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


Mass: 3333.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA
#2: DNA chain 5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'


Mass: 3361.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Interstrand Cross-Linked DNA

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
1422D NOESY

-
Sample preparation

DetailsContents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand ...Contents: The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand concentration in 0.3 mL containing 10 mM sodium phosphate (pH 7.4) and 100 mM NaCl.
Solvent system: both 1H2O (95%) and 2H2O (5%), and 99.9 % 2H2O.
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM NaCl 7.4 normal 293 K
2100 mM NaCl 7.4 normal 273 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

-
Processing

NMR softwareName: X-PLOR / Version: 3.8 / Developer: Brunger, A.T. / Classification: refinement
RefinementMethod: distance geometry simulated annealing, molecular dynamics
Software ordinal: 1
Details: A total of 449 restraints were used 243 non-exchangeable 53 exchangeable 44 hydrogen bond 109 dihedral angle
NMR representativeSelection criteria: closest to the average,lowest energy
NMR ensembleConformer selection criteria: the structure submitted is the lowest energy structure of a an ensemble of selected ten structures
Conformers calculated total number: 100 / 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