[English] 日本語
Yorodumi
- PDB-1gqu: Crystal structure of an alternating A-T oligonucleotide fragment ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gqu
TitleCrystal structure of an alternating A-T oligonucleotide fragment with Hoogsteen base pairing
ComponentsDNA (5'(*AP*TP*AP*UP*AP*T)-3')
KeywordsDNA / DNA/RNA / NEW DNA STRUCTURE / HOOGSTEEN BASE PAIRING
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsAbrescia, N.G.A. / Thompson, A. / Huynh-Dinh, T. / Subirana, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal Structure of an Antiparallel DNA Fragment with Hoogsteen Base Pairing
Authors: Abrescia, N.G.A. / Thompson, A. / Huynh-Dinh, T. / Subirana, J.A.
History
DepositionDec 5, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'(*AP*TP*AP*UP*AP*T)-3')
B: DNA (5'(*AP*TP*AP*UP*AP*T)-3')
C: DNA (5'(*AP*TP*AP*UP*AP*T)-3')
D: DNA (5'(*AP*TP*AP*UP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,4884
Polymers7,4884
Non-polymers00
Water84747
1
A: DNA (5'(*AP*TP*AP*UP*AP*T)-3')
B: DNA (5'(*AP*TP*AP*UP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,7442
Polymers3,7442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DNA (5'(*AP*TP*AP*UP*AP*T)-3')
D: DNA (5'(*AP*TP*AP*UP*AP*T)-3')


Theoretical massNumber of molelcules
Total (without water)3,7442
Polymers3,7442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)23.960, 48.950, 32.240
Angle α, β, γ (deg.)90.00, 93.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: DNA chain
DNA (5'(*AP*TP*AP*UP*AP*T)-3')


Mass: 1872.111 Da / Num. of mol.: 4 / 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 / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 % / Description: FOR MORE DETAILS ON DATA STATISTICS SEE PAPER
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 13 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.7 mMDNA duplex1drop
23 mMspermine1drop
39 mM1dropKCl
425 mMsodium cacodylate1droppH6.
537 %(v/v)MPD1drop
638 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.919,0.855
DetectorType: MARCCD / Detector: CCD / Date: Mar 15, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9191
20.8551
ReflectionResolution: 2.5→30 Å / Num. obs: 2591 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Rmerge(I) obs: 0.06
Reflection shellHighest resolution: 2.5 Å / % possible all: 68.6
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 68.6 % / Rmerge(I) obs: 0.175

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SCALEITdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FOR MORE DETAILS ON DATA STATISTICS SEE PAPER
RfactorNum. reflection% reflectionSelection details
Rwork0.22 ---
obs0.22 2547 97.2 %-
Rfree-240 9.2 %RANDOM
Solvent computationSolvent model: FLAT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 480 0 47 527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0089
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.61 Å / Num. reflection Rwork: 273 / Total num. of bins used: 8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1DNA-RNA.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Rfactor Rfree: 0.234 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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