[English] 日本語
Yorodumi
- PDB-1ycw: Clustered abasic lesions in dna: nmr solution structures of clust... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ycw
TitleClustered abasic lesions in dna: nmr solution structures of clustered bistranded-1 abasic lesion
Components
  • 5'-D(*CP*GP*CP*AP*TP*GP*(3DR)P*GP*TP*AP*CP*GP*C)-3'
  • 5'-D(*GP*CP*GP*TP*AP*CP*CP*(3DR)P*AP*TP*GP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX / ABASIC SITES / CLUSTERED DAMAGE / EXTRUDED RESIDUES / REDUCED AP SITE / FURAN / BISTRANDED ABASIC LESION
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsHazel, R.D. / de los Santos, C.
CitationJournal: Biochemistry / Year: 2008
Title: NMR solution structures of bistranded abasic site lesions in DNA.
Authors: Hazel, R.D. / Tian, K. / de Los Santos, C.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,6872
Polymers7,6872
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)5 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

-
Components

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


Mass: 3843.488 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SITES (3DR)
#2: DNA chain 5'-D(*GP*CP*GP*TP*AP*CP*CP*(3DR)P*AP*TP*GP*CP*G)-3'


Mass: 3843.488 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: RANDOMLY DESIGNED SEQUENCE CONTAINING STABLE ABASIC SITES (3DR)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1212D TOCSY
131DQF-COSY
141COSY, COSY45
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

-
Sample preparation

DetailsContents: 2mM DUPLEX, 25mM PHOSPHATE BUFFER, 50mM NaCl, 0.5mM EDTA
Solvent system: 25 mM PHOSPHATE BUFFER; PH 6.8; 50 mM NaCl; 0.5 mM EDTA.
Sample conditionsIonic strength: NOT DETERMINED / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1A. BRUNGERrefinement
Felix98data analysis
INSIGHT 95, MIDAS PLUS, CURVES 5data analysis
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO ...Details: 1) HEATING STAGE: FROM 150 TO 500 K IN 70PS. INTRODUCTION OF EXPERIMENTAL RESTRAINTS AT THE END OF THIS STAGE. 2) HIGH TEMPERATURE STAGE: 50 PS DYNAMICS AT 500K 3) COOLING STAGE: FROM 500 TO 300K IN 40PS. 4) EQUILIBRATION STAGE: 120PS DYNAMICS AT 300K
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 5

+
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