[English] 日本語
Yorodumi
- PDB-8w76: Crystal structure of d(CGTATACG)2 duplex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w76
TitleCrystal structure of d(CGTATACG)2 duplex
ComponentsDNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
KeywordsDNA / end-to-end junction / helix-helix junction
Function / homology: / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSatange, R.B. / Peng, C.L. / Hou, M.H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2628-M-005-001-MY4 Taiwan
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects.
Authors: Huang, S.C. / Chen, C.W. / Satange, R. / Hsieh, C.C. / Chang, C.C. / Wang, S.C. / Peng, C.L. / Chen, T.L. / Chiang, M.H. / Horng, Y.C. / Hou, M.H.
History
DepositionAug 30, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
D: DNA (5'-D(P*CP*GP*TP*AP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,0736
Polymers4,8532
Non-polymers2204
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-9 kcal/mol
Surface area3740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.614, 37.614, 77.994
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

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


Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.0mM Oligonucleotides, 50mM Bis-tris (pH 7.0), 20mM sodium chloride, 10mM calcium chloride, 80mM potassium chloride, 7mM manganese(II) chloride tetrahydrate, 10% PEG 2000, 50% Reservior PEG 2000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 1753 / % possible obs: 99.3 % / Redundancy: 9.5 % / Rsym value: 0.033 / Net I/σ(I): 25.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.810.50.1231620.99910.0390.1291.042100
2.8-2.9110.20.0971650.9980.9990.0310.1021.003100
2.91-3.0410.40.0781660.99910.0240.0821.057100
3.04-3.210.40.039172110.0120.0411.029100
3.2-3.49.80.021171110.0070.0230.99199.4
3.4-3.669.50.04167110.0130.0421.071100
3.66-4.038.60.0351780.99910.0120.0371.01100
4.03-4.619.40.031178110.010.0321.00598.9
4.61-5.89.40.032183110.0110.0341.02698.9
5.8-307.80.0372110.99910.0130.0391.00596.8

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→27.07 Å / SU ML: 0.1 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 169 9.95 %
Rwork0.2214 --
obs0.226 1698 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→27.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 328 4 6 338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004366
X-RAY DIFFRACTIONf_angle_d0.64560
X-RAY DIFFRACTIONf_dihedral_angle_d34.534154
X-RAY DIFFRACTIONf_chiral_restr0.0364
X-RAY DIFFRACTIONf_plane_restr0.00216
LS refinement shellResolution: 2.7→2.8 Å
RfactorNum. reflection% reflection
Rfree0.26 --
Rwork0.22 --
obs-1753 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1394-0.20110.09120.4366-0.17910.0787-0.0592-0.0909-0.2566-0.312-0.07940.1152-0.06870.5311-0.00030.2184-0.0521-0.0260.380.11180.27615.4932-1.552512.0478
20.26950.2652-0.05710.283-0.080.02510.12140.33840.02860.43350.08890.18430.53360.80450.02530.35060.09050.04180.49920.05030.352516.0412.62213.1368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 1 through 8 )
2X-RAY DIFFRACTION2chain 'D' and (resid 1 through 8 )

+
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