[English] 日本語
Yorodumi
- PDB-5ki4: Structural impact of single ribonucleotides in DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ki4
TitleStructural impact of single ribonucleotides in DNA
Components
  • DNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3')
  • DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')
KeywordsDNA
Function / homologyDNA
Function and homology information
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsEvich, M. / Spring-Connell, A.M. / Storici, F.
CitationJournal: Chembiochem / Year: 2016
Title: Structural Impact of Single Ribonucleotide Residues in DNA.
Authors: Evich, M. / Spring-Connell, A.M. / Storici, F. / Germann, M.W.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Nov 2, 2016Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3')
B: DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)5,4722
Polymers5,4722
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area830 Å2
ΔGint-4 kcal/mol
Surface area3610 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

-
Components

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


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D NOESY 250 ms
222isotropic12D NOESY
131isotropic12D Low Flip COSY
141isotropic22D 1H-13C HSQC
151isotropic12D constant time NOESY
161isotropic12D 1H-31P CORR
171isotropic12D NOESY 150 ms
181isotropic11D 1H
191isotropic11D 31P
2102isotropic11D 1H 1-1 jump and return

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM DNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 % 100% deuterium D20, 100 mM sodium chloride, 10 mM sodium phosphate, 100% D2O100% D2O, pH* 6.6D2O_sample100% D2O
solution21 mM DNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3'), 1 mM DNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3'), 100 mM sodium chloride, 10 mM sodium phosphate, 10 % 100% deuterium D2O, 90% H2O/10% D2O90% H2O, 10% D2O, pH 7H2O_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMDNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3')natural abundance1
1 mMDNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')natural abundance1
100 %D20100% deuterium1
100 mMsodium chloridenatural abundance1
10 mMsodium phosphatenatural abundance1
1 mMDNA (5'-D(*AP*TP*CP*CP*GP*GP*TP*AP*G)-3')natural abundance2
1 mMDNA (5'-D(*CP*TP*AP*CP*CP*GP*GP*AP*T)-3')natural abundance2
100 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
10 %D2O100% deuterium2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1110 mMD2O_conditions6.6 ambient atm294 K
2110 mMH2O_conditions7.0 ambient atm294 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance6001
Bruker AvanceIIIBrukerAvanceIII8502

-
Processing

NMR software
NameVersionDeveloperClassification
AMBER9Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
SPARKY3.33Goddardchemical shift assignment
TOPSPINBruker Biospincollection
CORMAThomas Jamesrefinement
MARDIGRASThomas Jamesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: matrix relaxation with MARDIGRAS
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 10 / Conformers submitted total number: 10

+
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