[English] 日本語
Yorodumi
- PDB-1vt8: Crystal structure of D(GGGCGCCC)-hexagonal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vt8
TitleCrystal structure of D(GGGCGCCC)-hexagonal form
ComponentsDNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsShakked, Z. / Guerstein-Guzikevich, G. / Eisenstein, M. / Frolow, F. / Rabinovich, D.
CitationJournal: Nature / Year: 1989
Title: The conformation of the DNA double helix in the crystal is dependent on its environment.
Authors: Shakked, Z. / Guerstein-Guzikevich, G. / Eisenstein, M. / Frolow, F. / Rabinovich, D.
History
DepositionDec 2, 1996Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*CP*GP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,8572
Polymers4,8572
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area3060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.620, 43.620, 41.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 2428.593 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 292 K
Details: MPD, Sodium Cacodylate, spermine, MgCl2, temperature 292K
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12WATER1311
25MPD1614
38MGCL21917
411SPERMINE_HCL112110
514NA CACODYLATE115113
617WATER118216
720MPD121219

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 2827 / Observed criterion σ(F): 2

-
Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementHighest resolution: 1.9 Å / σ(F): 1.9 /
RfactorNum. reflection
Rwork0.16 -
obs0.16 2827
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 322 0 97 419

+
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