[English] 日本語
Yorodumi
- PDB-8ask: Crystal structure of d(GCCCACCACGGC) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ask
TitleCrystal structure of d(GCCCACCACGGC)
Components
  • DNA (5'-D(P*GP*CP*CP*CP*AP*CP*CP*AP*CP*GP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*CP*GP*TP*GP*GP*TP*GP*GP*GP*C)-3')
KeywordsDNA / Ligand / Interaction
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.955 Å
AuthorsSbirkova-Dimitrova, H.I. / Shivachev, B.L. / Rusev, R. / Heroux, A. / Doukov, T. / Kuvandjiev, N.
Funding supportBulgaria, 1items
OrganizationGrant numberCountry
The Bulgarian National Science Fund (BNSF)KP-06-M31/1Bulgaria
CitationJournal: Crystals / Year: 2022
Title: Structural Characterization of Alzheimer DNA Promoter Sequences from the Amyloid Precursor Gene in the Presence of Thioflavin T and Analogs
Authors: Sbirkova-Dimitrova, H. / Rusew, R. / Kuvandjiev, N. / Heroux, A. / Doukov, T. / Shivachev, B.L.
History
DepositionAug 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: DNA (5'-D(P*GP*CP*CP*CP*AP*CP*CP*AP*CP*GP*GP*C)-3')
BBB: DNA (5'-D(P*GP*CP*CP*GP*TP*GP*GP*TP*GP*GP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,3292
Polymers7,3292
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-9 kcal/mol
Surface area4620 Å2
Unit cell
Length a, b, c (Å)64.490, 64.490, 46.190
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 3593.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: Synthesium (invertebrata)
#2: DNA chain DNA (5'-D(P*GP*CP*CP*GP*TP*GP*GP*TP*GP*GP*GP*C)-3')


Mass: 3735.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: Synthesium (invertebrata)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20%MPD, 120mMMgCl2, 60mM NaCaCo, 2mM Spermine

-
Data collection

DiffractionMean temperature: 270 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.95→35.59 Å / Num. obs: 2783 / % possible obs: 96.95 % / Redundancy: 9.2 % / CC1/2: 0.992 / Net I/σ(I): 2
Reflection shellResolution: 2.97→3.02 Å / Num. unique obs: 1399 / CC1/2: 0.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: X3DNA

Resolution: 2.955→35.59 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.891 / SU B: 27.017 / SU ML: 0.398 / Cross valid method: NONE / ESU R Free: 0.413
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2298 62 4.244 %
Rwork0.125 1399 -
all0.129 --
obs-1461 96.948 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 88.593 Å2
Baniso -1Baniso -2Baniso -3
1--0.113 Å2-0.057 Å20 Å2
2---0.113 Å20 Å2
3---0.368 Å2
Refinement stepCycle: LAST / Resolution: 2.955→35.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 492 0 0 492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.011550
X-RAY DIFFRACTIONr_bond_other_d0.0030.02266
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.168844
X-RAY DIFFRACTIONr_angle_other_deg1.7513630
X-RAY DIFFRACTIONr_chiral_restr0.0690.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02136
X-RAY DIFFRACTIONr_nbd_refined0.130.240
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2650.2300
X-RAY DIFFRACTIONr_nbtor_refined0.2560.2203
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.2159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.28
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1160.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3430.228
X-RAY DIFFRACTIONr_nbd_other0.3010.215
X-RAY DIFFRACTIONr_scbond_it4.6369.158550
X-RAY DIFFRACTIONr_scbond_other4.6079.157549
X-RAY DIFFRACTIONr_scangle_it6.76813.685844
X-RAY DIFFRACTIONr_scangle_other6.75613.685844
X-RAY DIFFRACTIONr_lrange_it8.35183.518738
X-RAY DIFFRACTIONr_lrange_other8.35183.506739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.955-3.0310.26440.285112X-RAY DIFFRACTION99.1453
3.031-3.11400.225107X-RAY DIFFRACTION100
3.114-3.2030.14940.19799X-RAY DIFFRACTION99.0385
3.203-3.3010.06320.2570X-RAY DIFFRACTION73.4694
3.301-3.4080.41750.21179X-RAY DIFFRACTION84.8485
3.408-3.5270.19160.18681X-RAY DIFFRACTION97.7528
3.527-3.6580.124100.16689X-RAY DIFFRACTION100
3.658-3.8060.06320.12885X-RAY DIFFRACTION98.8636
3.806-3.9730.14130.12987X-RAY DIFFRACTION100
3.973-4.1650.14170.11375X-RAY DIFFRACTION100
4.165-4.3870.23350.09471X-RAY DIFFRACTION100
4.387-4.6480.17130.09371X-RAY DIFFRACTION100
4.648-4.9630.24520.10967X-RAY DIFFRACTION100
4.963-5.3520.67210.13561X-RAY DIFFRACTION100
5.352-5.850.24420.20359X-RAY DIFFRACTION100
5.85-6.5180.13120.12252X-RAY DIFFRACTION100
6.518-7.4850.46420.12737X-RAY DIFFRACTION100
7.485-9.0670.33120.06844X-RAY DIFFRACTION100
9.067-12.42600.05734X-RAY DIFFRACTION100
12.426-35.5900.13719X-RAY DIFFRACTION100

+
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