[English] 日本語
Yorodumi
- PDB-8dx6: [C:Hg2+/Ag+:C--pH 5.5] Metal-mediated DNA base pair in tensegrity... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dx6
Title[C:Hg2+/Ag+:C--pH 5.5] Metal-mediated DNA base pair in tensegrity triangle in Ag+ and Hg2+ solution
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
  • DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA / Tensegrity triangle / self-assembling crystal / metal-mediated mismatch
Function / homologySILVER ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.34 Å
AuthorsLu, B. / Vecchioni, S. / Seeman, N.C. / Sha, R. / Ohayon, Y.P.
Funding support United States, France, 6items
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
National Aeronautic Space Administration (NASA, United States)2020 NASA Center Innovation Fund United States
CitationJournal: J.Am.Chem.Soc. / Year: 2023
Title: Heterobimetallic Base Pair Programming in Designer 3D DNA Crystals.
Authors: Lu, B. / Ohayon, Y.P. / Woloszyn, K. / Yang, C.F. / Yoder, J.B. / Rothschild, L.J. / Wind, S.J. / Hendrickson, W.A. / Mao, C. / Seeman, N.C. / Canary, J.W. / Sha, R. / Vecchioni, S.
History
DepositionAug 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8655
Polymers12,7574
Non-polymers1081
Water00
1
A: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')
B: DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)38,59615
Polymers38,27212
Non-polymers3243
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)107.801, 107.801, 90.309
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
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*AP*GP*CP*CP*TP*GP*TP*CP*TP*GP*GP*AP*CP*AP*TP*CP*A)-3')


Mass: 6448.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*CP*AP*CP*A)-3')


Mass: 2051.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-AG / SILVER ION


Mass: 107.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ag / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 7.92 Å3/Da / Density % sol: 84.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 40 mM Tris, 125 mM Magnesium sulfate, 12 uM silver nitrate, 24 uM mercury chloride
Temp details: 338-293 at 0.4/hr

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1.00743 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00743 Å / Relative weight: 1
ReflectionResolution: 5.31→64.91 Å / Num. obs: 2184 / % possible obs: 85.6 % / Redundancy: 10.6 % / Biso Wilson estimate: 367.75 Å2 / CC1/2: 1 / Net I/σ(I): 10.5
Reflection shellResolution: 5.31→6.17 Å / Num. unique obs: 438 / CC1/2: 0.127

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 5.34→32.87 Å / SU ML: 0.9164 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.0057
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2608 76 3.98 %
Rwork0.1936 1835 -
obs0.1955 1911 69.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 519.59 Å2
Refinement stepCycle: LAST / Resolution: 5.34→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 856 1 0 857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083956
X-RAY DIFFRACTIONf_angle_d1.05911467
X-RAY DIFFRACTIONf_chiral_restr0.0615167
X-RAY DIFFRACTIONf_plane_restr0.005742
X-RAY DIFFRACTIONf_dihedral_angle_d38.6978407
LS refinement shellResolution: 5.34→32.87 Å
RfactorNum. reflection% reflection
Rfree0.2608 76 -
Rwork0.1936 1835 -
obs--69.04 %
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)
12.04088872115-0.8636341888560.8430217353088.39543957844-1.966958863510.676292248404-1.04727378046-2.657631470450.4693361907230.0365328453942.378748788510.6686879667710.283610160407-0.5878073279151.868056811474.09817394373-0.111403094687-0.8948940627346.2427589872-1.63964179122.95647480743-14.8205089517-3.8397541863523.4987454265
21.052322290380.0807129864293-0.1727837204380.06497357419110.6021167901285.864166619820.7591333272650.826644873896-1.338585439150.6353082361430.740796137558-1.189899667032.103399414350.205894408502-0.09745499979731.94302607137-0.109055428933-3.127013668743.96984790798-0.773573619562.83121439952-14.0394560278-0.82331503751722.2392034431
30.4527103499010.262858319126-0.5953724649670.128235610771-0.3174840534340.763765662324-1.11823688805-1.80998235696-1.58305456619-0.62886466087-1.617108653943.444691935822.00041708524-4.85095679646-0.04000859057057.25039898361-0.7011653058730.01786798758695.382411827370.912193199274.43985204447-17.0109097116-21.262961159635.1063965478
41.988100001165.085665949755.0315248182.073118783711.815140219594.05774987666-3.839710441611.82522261736-0.737540896448-0.9524507652394.98940806015-1.30864652433-1.138790237441.458454490090.1734643949975.188012367780.2900442298263.121636413532.77273976901-0.1844635865277.43559209305-12.4740091219.45207273588.90064916486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 21)AA1 - 21
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 7)BB1 - 7
3X-RAY DIFFRACTION3(chain 'C' and resid 8 through 14)CC8 - 14
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 7)DD1 - 7

+
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