[English] 日本語
Yorodumi
- PDB-2d47: MOLECULAR STRUCTURE OF A COMPLETE TURN OF A-DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2d47
TitleMOLECULAR STRUCTURE OF A COMPLETE TURN OF A-DNA
ComponentsDNA (5'-D(*CP*CP*CP*CP*CP*GP*CP*GP*GP*GP*GP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologySPERMINE / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsVerdaguer, N. / Aymami, J. / Fernandez-Forner, D. / Fita, I. / Coll, M. / Huynh-Dinh, T. / Igolen, J. / Subirana, J.A.
CitationJournal: J.Mol.Biol. / Year: 1991
Title: Molecular structure of a complete turn of A-DNA.
Authors: Verdaguer, N. / Aymami, J. / Fernandez-Forner, D. / Fita, I. / Coll, M. / Huynh-Dinh, T. / Igolen, J. / Subirana, J.A.
History
DepositionOct 2, 1991Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 2, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DNA (5'-D(*CP*CP*CP*CP*CP*GP*CP*GP*GP*GP*GP*G)-3')
B: DNA (5'-D(*CP*CP*CP*CP*CP*GP*CP*GP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5333
Polymers7,3312
Non-polymers2021
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.200, 45.200, 65.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

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


Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H26N4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growMethod: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4CACL211
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 mMdodecamer1drop
230 mMsodium cacodylate1drop
35 mMcalcium chloride1drop
41.25 mMspermine tetrachloride1drop
55 %(v/v)MPD1drop
620 %MPD1reservoir
71

-
Data collection

DiffractionMean temperature: 293 K
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 2333 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.039

-
Processing

Software
NameVersionClassification
NUCLSQ(MODIFIED BY G.J.QUIGLEY)refinement
MODIFIEDBY G.J.QUIGLEYrefinement
RefinementResolution: 2→7 Å / σ(F): 3 /
RfactorNum. reflection
obs0.177 2082
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 14 107 607
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 7 Å / Num. reflection obs: 2082 / σ(F): 3 / Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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