[English] 日本語
Yorodumi
- PDB-1i0t: 0.6 A STRUCTURE OF Z-DNA CGCGCG -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1i0t
Title0.6 A STRUCTURE OF Z-DNA CGCGCG
Components5'-D(*CP*GP*CP*GP*CP*G)-3'
KeywordsDNA / Z-form double helix
Function / homologySPERMINE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.6 Å
AuthorsTereshko, V. / Wilds, C.J. / Minasov, G. / Prakash, T.P. / Maier, M.A. / Howard, A. / Wawrzak, Z. / Manoharan, M. / Egli, M.
CitationJournal: Nucleic Acids Res. / Year: 2001
Title: Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments.
Authors: Tereshko, V. / Wilds, C.J. / Minasov, G. / Prakash, T.P. / Maier, M.A. / Howard, A. / Wawrzak, Z. / Manoharan, M. / Egli, M.
History
DepositionJan 29, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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: 5'-D(*CP*GP*CP*GP*CP*G)-3'
B: 5'-D(*CP*GP*CP*GP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8233
Polymers3,6202
Non-polymers2021
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)18.316, 30.680, 42.491
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-SPM / SPERMINE


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


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.65 Å3/Da / Density % sol: 25.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: spermine, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298 K, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mMDNA1drop
240 mMalkali metal ions(chloride salt)1drop
320 mMalkaline cacodylate1drop
46 mMspermine1drop
510 mM1dropMgCl2
635 %MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.663 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.663 Å / Relative weight: 1
ReflectionResolution: 0.6→20 Å / Num. all: 57623 / Num. obs: 57623 / % possible obs: 96 % / Observed criterion σ(F): -3 / Rmerge(I) obs: 0.062

-
Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.185 -RANDOM
Rwork0.16 --
obs0.16 57623 -
all-57623 -
Refinement stepCycle: LAST / Resolution: 0.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 14 40 294
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_mcbond_it
X-RAY DIFFRACTIONs_scbond_it
X-RAY DIFFRACTIONs_mcangle_it
X-RAY DIFFRACTIONs_scangle_it

+
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