[English] 日本語
Yorodumi
- PDB-7urk: Self-assembling DNA tensegrity triangle motif with intercalating ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7urk
TitleSelf-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification
Components
  • DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
  • DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
KeywordsDNA / Tensegrity triangle / Cy3 / dye / self-assembly
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å
AuthorsSha, R. / Vecchioni, S.
Funding support United States, France, 5items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
Department of Energy (DOE, United States)DE-SC0007991 United States
National Science Foundation (NSF, United States)2106790 United States
Human Frontier Science Program (HFSP)RPG0010/2017 France
National Science Foundation (NSF, United States)DMR-1420073 United States
CitationJournal: To Be Published
Title: Self-assembling DNA tensegrity triangle motif with intercalating internal Cy3 modification
Authors: Sha, R. / Vecchioni, S.
History
DepositionApr 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: 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
A: DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)13,2254
Polymers13,2254
Non-polymers00
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

A: DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

A: DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')
B: DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')
C: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')
D: DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)39,67512
Polymers39,67512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)113.785, 113.785, 95.709
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*CP*A*(96T)P*GP*CP*CP*TP*GP*TP*A)-3')


Mass: 4115.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*CP*AP*CP*CP*GP*T)-3')


Mass: 2082.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*GP*CP*TP*GP*C)-3')


Mass: 4302.788 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 2724.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 8.41 Å3/Da / Density % sol: 86.36 % / Description: rhombohedral
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 120 mM Tris, 583 mM ammonium sulfate, 37.5 mM magnesium acetate, 60 mM acetic acid, 6 mM EDTA
Temp details: 338-293 at 0.4/hr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.18076 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 3.119→34.33 Å / Num. obs: 4656 / % possible obs: 75 % / Redundancy: 9.9 % / Biso Wilson estimate: 113.93 Å2 / CC1/2: 1 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
3.119-3.4392.92330.8571
10.101-34.32846.423011

-
Processing

Software
NameVersionClassification
PHASER1.18.2_3874phasing
PHENIX1.18.2_3874refinement
autoPROCdata reduction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBI

3gbi


Resolution: 3.12→34.33 Å / SU ML: 0.116 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 26.1539
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1566 458 4.92 %
Rwork0.155 8849 -
obs0.1551 4656 56.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 169.8 Å2
Refinement stepCycle: LAST / Resolution: 3.12→34.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 870 0 0 870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153970
X-RAY DIFFRACTIONf_angle_d1.59021483
X-RAY DIFFRACTIONf_chiral_restr0.0717162
X-RAY DIFFRACTIONf_plane_restr0.064445
X-RAY DIFFRACTIONf_dihedral_angle_d37.4132427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.12-3.570.3859560.275666X-RAY DIFFRACTION13.18
3.57-4.50.33041420.29592978X-RAY DIFFRACTION56.89
4.5-34.330.11662600.12755205X-RAY DIFFRACTION99.22
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)
15.591331693025.295573626595.957462816835.296867138564.96538594627.99591602622-1.143946637711.99123483145-0.0507854777552-0.8750592508290.771240418841-2.18037915394-2.27911184820.607776657116-0.457191844132.02165501383-0.536794489834-0.6272194755472.41149290224-0.136515854381.2845469689432.33.9770.14
28.334703244810.5859550727410.6404702883248.20155113507-6.442713082085.334179510550.560849009458-0.1197227928060.548137952043-1.06189864134-0.5112683150930.5902210342660.962545549017-0.7418248954680.09838438538051.33714172772-0.02779727938120.1376377594841.96926972944-0.360807263420.9694832171213.0381.613-10.944
38.952252711342.182642229631.621405431559.615540517035.65717703288.477067037791.54865739260.23424197636-0.297506510515-0.296632896331-0.479695920642-1.502351532280.474324583169-0.227632031315-1.072842843411.109252298310.208542249829-0.1506434909711.44051451386-0.378515122691.6869316059925.008-2.622-12.748
45.508993423270.6560892988942.12186650475.043426883390.7973605439192.637043125180.570680365471-0.2497969967571.05624689115-0.5655769064240.364695140637-0.73547379414-0.402604680466-0.277573464467-1.027757571511.610878396070.1351079431720.3823213267281.81532130841-0.1037097142060.85231858273219.3932.764-18.749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 101:113 )A101 - 113
2X-RAY DIFFRACTION2( CHAIN B AND RESID 105:111 )B105 - 111
3X-RAY DIFFRACTION3( CHAIN C AND RESID 101:114 )C101 - 114
4X-RAY DIFFRACTION4( CHAIN D AND RESID 113:121 )D113 - 121

+
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