[English] 日本語
Yorodumi
- PDB-8ash: Crystal structure of d(CCGGGGTACCCCGG) with XRB -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ash
TitleCrystal structure of d(CCGGGGTACCCCGG) with XRB
ComponentsDNA (5'-D(*CP*CP*GP*GP*GP*GP*TP*AP*CP*CP*CP*CP*GP*G)-3')
KeywordsDNA / Ligand / Interaction
Function / homologyChem-O89 / DNA / DNA (> 10)
Function and homology information
Biological speciesDNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.837 Å
AuthorsSbirkova-Dimitrova, H.I. / Shivachev, B.L. / Rusev, R. / Kuvandjiev, N. / Heroux, A. / Doukov, T.
Funding supportBulgaria, 1items
OrganizationGrant numberCountry
Bulgarian National Science FundKP-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 1.1Jan 31, 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(*CP*CP*GP*GP*GP*GP*TP*AP*CP*CP*CP*CP*GP*G)-3')
BBB: DNA (5'-D(*CP*CP*GP*GP*GP*GP*TP*AP*CP*CP*CP*CP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8763
Polymers8,5662
Non-polymers3101
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-4 kcal/mol
Surface area5350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.760, 41.760, 88.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 4282.768 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DNA molecule (others) / Production host: Synthesium (invertebrata)
#2: Chemical ChemComp-O89 / 4-[(~{E})-(3,6-dimethyl-1,3-benzothiazol-2-yl)iminomethyl]-~{N},~{N}-dimethyl-aniline


Mass: 310.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 8%MPD, 1mM BaCl2, 5mM 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 / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.837→37.8 Å / Num. obs: 7419 / % possible obs: 98.83 % / Redundancy: 10.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Rrim(I) all: 0.12 / Net I/σ(I): 50.8
Reflection shellResolution: 1.837→1.885 Å / Num. unique obs: 453 / CC1/2: 0.716 / % possible all: 90.94

-
Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WV7

5wv7


Resolution: 1.837→37.8 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.929 / SU B: 1.111 / SU ML: 0.033 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1927 361 4.949 %
Rwork0.1415 6934 -
all0.144 --
obs-7295 98.835 %
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: 43.764 Å2
Baniso -1Baniso -2Baniso -3
1-0.012 Å2-0 Å2-0 Å2
2--0.012 Å2-0 Å2
3----0.024 Å2
Refinement stepCycle: LAST / Resolution: 1.837→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 568 22 0 590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.011660
X-RAY DIFFRACTIONr_bond_other_d0.0030.02332
X-RAY DIFFRACTIONr_angle_refined_deg1.7411.221012
X-RAY DIFFRACTIONr_angle_other_deg1.3833776
X-RAY DIFFRACTIONr_chiral_restr0.1520.284
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02374
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02169
X-RAY DIFFRACTIONr_nbd_refined0.0840.250
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.2352
X-RAY DIFFRACTIONr_nbtor_refined0.2690.2214
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0580.2126
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0350.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1530.215
X-RAY DIFFRACTIONr_nbd_other0.2510.279
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4760.21
X-RAY DIFFRACTIONr_scbond_it1.8554.371660
X-RAY DIFFRACTIONr_scbond_other1.8564.392661
X-RAY DIFFRACTIONr_scangle_it2.476.5011012
X-RAY DIFFRACTIONr_scangle_other2.4696.5221013
X-RAY DIFFRACTIONr_lrange_it5.78739.678880
X-RAY DIFFRACTIONr_lrange_other5.78439.909881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.837-1.8850.192290.142453X-RAY DIFFRACTION90.9434
1.885-1.9360.542280.433484X-RAY DIFFRACTION99.2248
1.936-1.9920.145230.126485X-RAY DIFFRACTION99.8035
1.992-2.0530.131270.099453X-RAY DIFFRACTION100
2.053-2.120.132210.094448X-RAY DIFFRACTION100
2.12-2.1950.091230.078442X-RAY DIFFRACTION100
2.195-2.2770.089220.066425X-RAY DIFFRACTION100
2.277-2.370.164200.108403X-RAY DIFFRACTION99.7642
2.37-2.4750.109230.115396X-RAY DIFFRACTION99.7619
2.475-2.5950.133160.089377X-RAY DIFFRACTION100
2.595-2.7350.072190.079359X-RAY DIFFRACTION99.7361
2.735-2.8990.085180.076333X-RAY DIFFRACTION99.1525
2.899-3.0980.13790.091324X-RAY DIFFRACTION97.9412
3.098-3.3450.138160.132311X-RAY DIFFRACTION99.6951
3.345-3.6610.131100.126284X-RAY DIFFRACTION99.3243
3.661-4.0880.107150.109258X-RAY DIFFRACTION98.913
4.088-4.7120.071140.076233X-RAY DIFFRACTION98.4064
4.712-5.7480.152150.109195X-RAY DIFFRACTION99.5261
5.748-8.0370.3150.242166X-RAY DIFFRACTION97.7143
8.037-37.82.03580.656105X-RAY DIFFRACTION95.7627

+
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