[English] 日本語
Yorodumi
- PDB-6udn: Crystal Structure of a Self-Assembling DNA Scaffold Containing TA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6udn
TitleCrystal Structure of a Self-Assembling DNA Scaffold Containing TA Sticky Ends and Rhombohedral Symmetry
Components
  • DNA (5'-D(*TP*AP*CP*TP*GP*AP*CP*TP*CP*AP*TP*GP*CP*TP*CP*AP*TP*CP*TP*GP*A)-3')
  • DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')
  • DNA (5'-D(P*GP*TP*CP*AP*G)-3')
KeywordsDNA / Self-Assembly / DNA Nanotechnology / DNA Scaffold / Crystal Lattice
Function / homologyARSENIC / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsSimmons, C.R. / MacCulloch, T. / Stephanopoulos, N. / Yan, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1360635 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM104960 United States
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail.
Authors: Simmons, C.R. / MacCulloch, T. / Zhang, F. / Liu, Y. / Stephanopoulos, N. / Yan, H.
History
DepositionSep 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,9446
Polymers12,7944
Non-polymers1502
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.091, 116.091, 45.001
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

-
Components

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


Mass: 6373.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*AP*GP*CP*AP*TP*GP*A)-3')


Mass: 2146.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*TP*CP*AP*GP*AP*TP*G)-3')


Mass: 2754.835 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*CP*AP*G)-3')


Mass: 1520.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-ARS / ARSENIC


Mass: 74.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: As
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.56 Å3/Da / Density % sol: 73.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.5 mL of 0.05 M cacodylate pH 6.0 with 20 mM MgCl2, 1.0 mM spermine, and 15% ethanol was added to the reservoir with 2 uL added to the drop containing 4 uL of DNA stock.
Temp details: Temperature gradient generated from 60 to 25 C at 0.3 degrees per hour

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 6933 / % possible obs: 99.9 % / Redundancy: 10 % / Biso Wilson estimate: 94.74 Å2 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.032 / Rrim(I) all: 0.1 / Χ2: 2.659 / Net I/σ(I): 10.9 / Num. measured all: 69622
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.649.80.9943670.7540.3341.050.44100
2.64-2.699.60.7243020.8520.2460.7650.445100
2.69-2.749.50.6343880.8710.2170.670.465100
2.74-2.89.90.4573120.9140.1520.4810.481100
2.8-2.86100.4423680.9450.1470.4660.501100
2.86-2.9310.40.3123410.9750.1010.3280.538100
2.93-310.50.2323410.9840.0750.2440.604100
3-3.0810.20.1693300.9940.0550.1780.935100
3.08-3.1710.20.1283610.9940.0420.1351.518100
3.17-3.289.60.13630.9920.0360.1072.609100
3.28-3.399.40.1253170.9950.0460.1342.75699.1
3.39-3.539.90.1013650.9950.0340.1063.29899.7
3.53-3.6910.50.1063400.9940.0340.1113.472100
3.69-3.8810.40.0983540.9950.0320.1033.573100
3.88-4.1310.30.0943530.9950.0310.0994.201100
4.13-4.459.70.0873530.9940.0290.0924.13100
4.45-4.8910.30.0933420.9940.030.0984.648100
4.89-5.610.60.0893460.9920.0290.0945.238100
5.6-7.059.80.0863370.9950.0290.094.912100
7.05-5010.10.0873530.9910.030.0927.89599.7

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6U40

6u40


Resolution: 2.602→23.703 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 37.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 347 5.05 %
Rwork0.2339 6519 -
obs0.235 6866 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.02 Å2 / Biso mean: 101.729 Å2 / Biso min: 54.74 Å2
Refinement stepCycle: final / Resolution: 2.602→23.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 2 0 857
Biso mean--141.01 --
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006956
X-RAY DIFFRACTIONf_angle_d0.8471467
X-RAY DIFFRACTIONf_chiral_restr0.05166
X-RAY DIFFRACTIONf_plane_restr0.00542
X-RAY DIFFRACTIONf_dihedral_angle_d37.857406
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.602-3.27690.35931720.33763254
3.2769-23.7030.23621750.21663265

+
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