[English] 日本語
Yorodumi
- PDB-2kaz: Folding topology of a bimolecular DNA quadruplex containing a sta... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kaz
TitleFolding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop
Components5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
KeywordsDNA / bimolecular DNA quadruplex / DNA hairpins / quadruplex
Function / homology: / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / molecular dynamics
AuthorsBalkwill, G.D. / Garner, T.P. / Williams, H.E.L. / Searle, M.S.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop
Authors: Balkwill, G.D. / Garner, T.P. / Williams, H.E. / Searle, M.S.
History
DepositionNov 18, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 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 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
B: 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3044
Polymers8,2252
Non-polymers782
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)5 / 6000structures with acceptable covalent geometry
RepresentativeModel #1closest to the average

-
Components

#1: DNA chain 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'


Mass: 4112.669 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H NOESY
1312D 1H-1H TOCSY

-
Sample preparation

DetailsContents: 2 mM DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'), 10 mM K+, 10 % D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
2 mMDNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3')1
10 mMK1
10 %D2O1
Sample conditionsIonic strength: 10 / pH: 7.85 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

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

-
Processing

NMR software
NameVersionDeveloperClassification
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmstructure solution
Amber8Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
TopSpin2.1Bruker Biospinprocessing
TopSpin2.1Bruker Biospincollection
MOLMOL2kKoradi, Billeter and Wuthrichdata analysis
CCPNMR1.16CCPNchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Molecular dynamics on selected model. Conformers selected from the last 200ps of rMD. 5 structures selected based on a cluster analysis to group structures by RMSD.
NMR constraintsNOE constraints total: 503 / NOE intraresidue total count: 248 / NOE long range total count: 47 / NOE medium range total count: 35 / NOE sequential total count: 173
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry
Conformers calculated total number: 6000 / 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