[English] 日本語
Yorodumi
- PDB-272d: PARALLEL AND ANTIPARALLEL (G.GC)2 TRIPLE HELIX FRAGMENTS IN A CRY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 272d
TitlePARALLEL AND ANTIPARALLEL (G.GC)2 TRIPLE HELIX FRAGMENTS IN A CRYSTAL STRUCTURE
ComponentsDNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / INTERMOLECULAR BASE TRIPLET / OVERHANGING BASES
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsVlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
CitationJournal: Science / Year: 1996
Title: Parallel and antiparallel (G.GC)2 triple helix fragments in a crystal structure.
Authors: Vlieghe, D. / Van Meervelt, L. / Dautant, A. / Gallois, B. / Precigoux, G. / Kennard, O.
History
DepositionJul 9, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 20, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). TWO TYPES OF TRIPLEXES CAN BE GENERATED - PARALLEL TRIPLEX AND ANTIPARALLEL TRIPLEX. ONLY THE SYMMETRY OPERATIONS WHICH GENERATE THE PARALLEL TRIPLEX ARE SHOWN IN REMARK 350. THE PARALLEL TRIPLEX IS GENERATED BY APPLYING SYMMETRY OPERATION 1/2-X, 1-Y, 1/2+Z. THE ANTIPARALLEL TRIPLEX IS GENERATED BY APPLYING SYMMETRY OPERATION 1-X, 1/2+Y, 1/2-Z.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)6,1702
Polymers6,1702
Non-polymers00
Water79344
1
A: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')

A: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')
B: DNA (5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)12,3404
Polymers12,3404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Unit cell
Length a, b, c (Å)26.250, 36.820, 53.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 3085.029 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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 Å3/Da / Density % sol: 38.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 289.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 16 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 mMDNA1drop
243 mM1dropMgCl2
30.6 mMspermine1drop
43 %MPD1drop
540 %MPD1reservoir
61

-
Data collection

DiffractionAmbient temp details: ROOM TEMPERATURE
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: D41A
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→14.5 Å / Num. all: 12303 / Num. obs: 3534 / % possible obs: 94.6 % / Redundancy: 3 % / Rsym value: 0.046 / Net I/σ(I): 5.4
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.193 / % possible all: 86.3
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 14.5 Å / % possible obs: 94.6 % / Redundancy: 3 % / Num. measured all: 12303 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.1 Å / % possible obs: 86.3 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 3.8

-
Processing

Software
NameVersionClassification
AMoRE(J. NAVAZA)phasing
SHELXL-93refinement
IPMOSFLMdata reduction
ABSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→10 Å / Num. parameters: 1818 / Num. restraintsaints: 1990 / σ(F): 0 /
RfactorNum. reflection
obs0.209 3514
all-3514
Solvent computationSolvent model: BABINET'S PRINCIPLE
Displacement parametersBiso mean: 30.6 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 410 0 44 454
Software
*PLUS
Name: SHELXL-93 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 3212 / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.6 Å2

+
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