[English] 日本語
Yorodumi
- PDB-2lib: DNA sequence context conceals alpha anomeric lesion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lib
TitleDNA sequence context conceals alpha anomeric lesion
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*CP*(A3A)P*GP*GP*AP*CP*G)-3')
KeywordsDNA / Alpha anomeric adenosine / DNA damage / Flanking sequence effects / Structural perturbation / Structural distortion / Minor groove distortion / Endonuclease IV / Enzyme recognition / Helical axis kink / Enzyme modulation / DNA repair / DNA perturbation
Function / homologyDNA
Function and homology information
MethodSOLUTION NMR / restrained molecular dynamics
Model detailslowest AMBER violations, model 1
AuthorsJohnson, C.N. / Spring, A.M. / Cunningham, R.P. / Germann, M.W.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: DNA sequence context conceals alpha-anomeric lesions.
Authors: Johnson, C.N. / Spring, A.M. / Desai, S. / Cunningham, R.P. / Germann, M.W.
History
DepositionAug 27, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*TP*CP*CP*(A3A)P*GP*GP*AP*CP*G)-3')
B: DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0912
Polymers6,0912
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)1 / 10lowest AMBER violations
RepresentativeModel #1lowest amber violations

-
Components

#1: DNA chain DNA (5'-D(*GP*TP*CP*CP*(A3A)P*GP*GP*AP*CP*G)-3')


Mass: 3070.018 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')


Mass: 3020.979 Da / Num. of mol.: 1 / Source method: obtained synthetically

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1111-1 jump return
1211D NOE
1311-1 NOESY 2D 150 ms
242Low Flip COSY
252TOCYS
2622D 1H 1H NOESY 75 ms
2722D 1H 1H NOESY 125 ms
2822D 1H-1H NOESY 250 ms
292Constant Time COSY
21022D 1H-13C HSQC
21122D 1H-31P CORR
21221D 31P

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 10 % D2O, 0.2 uM DSS, 2 mM EDTA, 90% H2O/10% D2O90% H2O/10% D2O
20.75 mM DNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3'), 0.75 mM DNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3'), 10 mM sodium phosphate, 50 mM sodium chloride, 100 % D2O, 0.2 uM DSS, 2 mM EDTA, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
0.75 mMDNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3')-11
0.75 mMDNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')-21
10 mMsodium phosphate-31
50 mMsodium chloride-41
10 %D2O-51
0.2 uMDSS-61
2 mMEDTA-71
0.75 mMDNA (5'-D(*GP*TP*CP*CP*A3A*GP*GP*AP*CP*G)-3')-82
0.75 mMDNA (5'-D(*CP*GP*TP*CP*CP*TP*GP*GP*AP*C)-3')-92
10 mMsodium phosphate-102
50 mMsodium chloride-112
100 %D2O-122
0.2 uMDSS-132
2 mMEDTA-142
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 6.65 ambient 276 K
250 ambient 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
AMBER9Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmstructure solution
SPARKY3.3Goddardchemical shift assignment
TOPSPINBruker Biospindata analysis
CORMAThomas Jamesstructure solution
MARDGIRASThomas Jamesstructure solution
CURVES5.1Richard Laveryanalysis
CURVES5.1Heinz Sklenaranalysis
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: restrained molecular dynamics / Software ordinal: 1
Details: CORMA AMBER MARDIGRAS cycles with restrained molecular dynamics
NMR constraintsNOE constraints total: 246
NMR representativeSelection criteria: lowest amber violations
NMR ensembleConformer selection criteria: lowest AMBER violations / Conformers calculated total number: 10 / 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://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