[English] 日本語
Yorodumi
- PDB-6dkl: Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dkl
TitleCrystal Structure of a Rationally Designed Six-Fold Symmetric DNA Scaffold
Components
  • DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')
  • DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')
  • DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')
KeywordsDNA / DNA Nanotechnology / Structural DNA Nanotechnology / self-assembly / crystal design / DNA crystals
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.034 Å
AuthorsSimmons, C.R. / Zhang, F. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
National Science Foundation (NSF, United States)1360635 United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry.
Authors: Zhang, F. / Simmons, C.R. / Gates, J. / Liu, Y. / Yan, H.
History
DepositionMay 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.408, 68.408, 143.222
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

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


Mass: 2764.837 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3')


Mass: 2973.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3')


Mass: 3371.193 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 50 mM Cacodylate pH 6.0, 10 mM MgCl2, 200 mM sodium citrate, 5% isopropanol
Temp details: Temperature gradient was generated from 60C-25C for .3 degrees per hour.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.034→50 Å / Num. obs: 6788 / % possible obs: 91.8 % / Redundancy: 6.8 % / CC1/2: 0.98 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.115 / Net I/σ(I): 42.1
Reflection shellResolution: 3.034→3.1 Å / Num. unique obs: 252 / CC1/2: 0.93 / Rpim(I) all: 0.2

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.034→37.1758 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 41.42
RfactorNum. reflection% reflection
Rfree0.2339 660 10 %
Rwork0.2278 --
obs0.2284 6598 89.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.034→37.1758 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 851 0 0 851
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008952
X-RAY DIFFRACTIONf_angle_d0.9551461
X-RAY DIFFRACTIONf_dihedral_angle_d32.543400
X-RAY DIFFRACTIONf_chiral_restr0.057164
X-RAY DIFFRACTIONf_plane_restr0.00642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0342-3.26830.3872960.3426894X-RAY DIFFRACTION67
3.2683-3.5970.28441210.24041133X-RAY DIFFRACTION84
3.597-4.11690.2891470.28851273X-RAY DIFFRACTION98
4.1169-5.18460.30821510.2881318X-RAY DIFFRACTION100
5.1846-37.1730.1811450.1891320X-RAY DIFFRACTION98

+
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