[English] 日本語
Yorodumi
- PDB-5eos: Crystallizing Strained DNA: Self-Assembly of 3D Crystals Containi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eos
TitleCrystallizing Strained DNA: Self-Assembly of 3D Crystals Containing a Torsionally-Stressed Component
Components
  • DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
  • DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
  • DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
KeywordsDNA / DNA nanotechnology / torsionally strained DNA / DNA lattices
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.7 Å
AuthorsHernandez, C. / Birktoft, J.J. / Seeman, N.C.
CitationJournal: Cell Chem Biol / Year: 2017
Title: Self-Assembly of 3D DNA Crystals Containing a Torsionally Stressed Component.
Authors: Hernandez, C. / Birktoft, J.J. / Ohayon, Y.P. / Chandrasekaran, A.R. / Abdallah, H. / Sha, R. / Stojanoff, V. / Mao, C. / Seeman, N.C.
History
DepositionNov 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.classification
Revision 1.2Jun 24, 2020Group: Derived calculations
Category: ndb_struct_na_base_pair / ndb_struct_na_base_pair_step ...ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / struct_conn / struct_conn_type
Revision 1.3Mar 6, 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*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)12,7974
Polymers12,7974
Non-polymers00
Water0
1
A: DNA (5'-D(P*GP*AP*GP*CP*AP*GP*CP*TP*GP*TP*G)-3')
D: DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')
B: DNA (5'-D(*TP*CP*TP*GP*AP*TP*GP*TP*GP*CP*TP*GP*C)-3')
C: DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')

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

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


Theoretical massNumber of molelcules
Total (without water)38,39212
Polymers38,39212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Unit cell
Length a, b, c (Å)110.011, 110.011, 83.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsThe asymmetric unit is comprised of the first 11 nucleotides of the full #1 strand (chain A), by the last 10 residues of the full #1 strand (chain C), by the first 8 nucleotides of the #2 strand (chain D) and by #3 strand (chain B). Chains A (First 11 residues of strand #1) and C (next 10 residues of strand #1) together form the first DNA strand (#1) of the experiment. This DNA strand spans two asymmetric units-hence it was divided into the current chains A and C for convenient representation and crystallographic computing. Chain A (1_555) is covalently linked to chain C of another asymmetric unit (3_555); and chain C (1_555) is covalently linked to chain A of another asymmetric unit (2_555). The #2 strand form a circular DNA molecule as a consequence of internal 3-fold symmetry of the triangle chain D in the asymmetric unit represents one of these repeating units. It has 3 symmetric and sequential repeating units that are covalently linked to each other via the O3' end of residue 13D to the O5' end of residue 6D; chain D (1_555) is covalently linked to chain D of two neighboring asymmetric units (2_555) and (3_555). The selection of residues from the DNA #2 and #3 are dictated by their proximity (base pairing) to chains A and C. Chain B in the asymmetric unit represents the third of these repeating units.

-
Components

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


Mass: 3414.234 Da / Num. of mol.: 1
Fragment: The first 11 residues the DNA molecule used in the experiment
Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*T)-3')


Mass: 2371.582 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*CP*TP*GP*C)-3')


Mass: 3973.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*AP*CP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 3038.020 Da / Num. of mol.: 1
Fragment: The second 10 residues the DNA molecule used in the experiment
Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 64.6 % / Description: rhombohedral
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Grown by vapor diffusion while treated with a controlled temperature gradient from 333 degs to 277 degs. Ammonium Sulfate, magnesium chloride, Na Cacodylate, magnesium acetate, TRIS
PH range: 7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1, 1.7
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.71
ReflectionResolution: 4.7→27.5 Å / Num. obs: 4338 / % possible obs: 95 % / Redundancy: 1.8 % / Net I/σ(I): 2.6
Reflection shellResolution: 4.75→4.85 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.01 / Mean I/σ(I) obs: 2 / % possible all: 90

-
Processing

Software
NameVersionClassification
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 4.7→27.5 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 46.89
RfactorNum. reflection% reflection
Rfree0.2101 433 9.98 %
Rwork0.19 --
obs0.1924 4338 95.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 371.51 Å2 / Biso mean: 317.8413 Å2 / Biso min: 272.89 Å2
Refinement stepCycle: final / Resolution: 4.7→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 858 0 0 858
Num. residues----42

+
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