[English] 日本語
Yorodumi
- PDB-1cgc: DOUBLE HELIX CONFORMATION GROOVE DIMENSIONS AND LIGAND BINDING PO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cgc
TitleDOUBLE HELIX CONFORMATION GROOVE DIMENSIONS AND LIGAND BINDING POTENTIAL OF A G/C-STRETCH IN B-DNA
ComponentsDNA (5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsHeinemann, U. / Bansal, M.
Citation
Journal: EMBO J. / Year: 1992
Title: Double helix conformation, groove dimensions and ligand binding potential of a G/C stretch in B-DNA.
Authors: Heinemann, U. / Alings, C. / Bansal, M.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: C-C-A-G-G-C-m5C-T-G-C: Helical Fine Structure, Hydration, and Comparison with C-C-A-G-G-C-C-T-G-G
Authors: Heinemann, U. / Hahn, M.
#2: Journal: Embo J. / Year: 1991
Title: The Conformation of a B-DNA Decamer Is Mainly Determined by Its Sequence and Not by Crystal Environment
Authors: Heinemann, U. / Alings, C.
#3: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Study of One Turn of G/C-Rich B-DNA
Authors: Heinemann, U. / Alings, C.
History
DepositionJan 15, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 15, 1993Provider: 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 7, 2024Group: 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(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')
B: DNA (5'-D(*CP*CP*GP*GP*CP*GP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.070, 54.070, 44.590
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 3046.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7 / Details: pH 7.00, MICRODIALYSIS, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2BIS-TRIS-PROPANE_HCL11
3MGCL211
4WATER12
5MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
12 mMDNA1
210 mMTris-HCl1
3150 mM1MgCl2
410 mMTris-HCl1
5150 mM1MgCl2
624 %(v/v)MPD12

-
Data collection

Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS CAD4 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. all: 3078 / Num. obs: 2086 / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / % possible obs: 78 % / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.5 Å / % possible obs: 68 %

-
Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 1 /
RfactorNum. reflection
obs0.167 2019
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 404 0 47 451
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_plane_restr0.0190.03
X-RAY DIFFRACTIONn_chiral_restr0.0690.1

+
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