[English] 日本語
Yorodumi
- PDB-1r41: Crystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effect... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1r41
TitleCrystal structures of d(Gm5CGm5CGCGC) and d(GCGCGm5CGm5C): Effects of methylation on alternating DNA octamers
Components5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'
KeywordsDNA
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Molecular Placement / Resolution: 1.9 Å
AuthorsShi, K. / Pan, B. / Tippin, D. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of d(Gm5)CGm5CGCGC) and d(GCGCGm5CGm5C): effects of methylation on alternating DNA octamers.
Authors: Shi, K. / Pan, B. / Tippin, D. / Sundaralingam, M.
History
DepositionOct 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'


Theoretical massNumber of molelcules
Total (without water)2,4571
Polymers2,4571
Non-polymers00
Water34219
1
A: 5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'

A: 5'-D(*GP*CP*GP*CP*GP*(5CM)P*GP*(5CM))-3'


Theoretical massNumber of molelcules
Total (without water)4,9132
Polymers4,9132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)43.12, 43.12, 24.77
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

-
Components

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


Mass: 2456.647 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA Synthesizer
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.26 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: cacodylate, magnesium chloride, spermine tetrachloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1cacodylate11
2magnesium chloride11
3spermine tetrachloride11
4H2O11
5cacodylate12
6magnesium chloride12
7spermine tetrachloride12
8H2O12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMDNA1drop
225 mMsodium cacodylate1droppH6.0
31 mM1dropMgCl2
40.5 mMspermine tetrachloride1drop
540 %MPD1reservoir
61
71
81

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→19.23 Å / Num. obs: 2192
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 10 Å / % possible obs: 86.5 % / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
% possible obs: 84.8 % / Rmerge(I) obs: 0.309

-
Processing

RefinementMethod to determine structure: Molecular Placement / Resolution: 1.9→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorSelection details
Rfree0.198 RANDOM
Rwork0.183 -
all0.204 -
obs0.183 -
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 163 0 19 182
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.219 / Rfactor Rwork: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.048
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg5.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.376 / Rfactor Rwork: 0.351

+
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://pdbjlvh1.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