[English] 日本語
Yorodumi
- PDB-8tdy: 16mer self-complementary duplex RNA with D:U pair sequence 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tdy
Title16mer self-complementary duplex RNA with D:U pair sequence 1
ComponentsRNA
KeywordsRNA / Diaminopurine / Non-canonical base pair
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsFang, Z. / Jia, X. / Szostak, J.W.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2104708 United States
Simons Foundation290363 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Diaminopurine in Nonenzymatic RNA Template Copying.
Authors: Jia, X. / Fang, Z. / Kim, S.C. / Ding, D. / Zhou, L. / Szostak, J.W.
History
DepositionJul 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2024Group: Database references / Category: 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: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,1473
Polymers5,0981
Non-polymers492
Water1,08160
1
A: RNA
hetero molecules

A: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2936
Polymers10,1962
Non-polymers974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3190 Å2
ΔGint-26 kcal/mol
Surface area5580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.146, 41.146, 125.047
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

21A-235-

HOH

31A-236-

HOH

41A-239-

HOH

51A-252-

HOH

-
Components

#1: RNA chain RNA


Mass: 5098.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 80 mM Strontium chloride hexahydrate, 20 mM Magnesium chloride hexahydrate, 40 mM Sodium cacodylate trihydrate pH 7.0, 20% v/v (+/-)-2-Methyl-2,4-pentanediol, 12 mM Spermine

-
Data collection

DiffractionMean temperature: 99 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.038413 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038413 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 5058 / % possible obs: 99.6 % / Redundancy: 8.5 % / Biso Wilson estimate: 10.08 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.035 / Rrim(I) all: 0.104 / Χ2: 0.951 / Net I/σ(I): 4.2
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 483 / CC1/2: 0.902 / CC star: 0.974 / Rpim(I) all: 0.225 / Rrim(I) all: 0.569 / Χ2: 1.021 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→41.68 Å / SU ML: 0.1547 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.6202
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2238 235 4.75 %
Rwork0.1962 4711 -
obs0.1975 4946 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.06 Å2
Refinement stepCycle: LAST / Resolution: 1.66→41.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 337 2 60 399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049376
X-RAY DIFFRACTIONf_angle_d0.9549584
X-RAY DIFFRACTIONf_chiral_restr0.042178
X-RAY DIFFRACTIONf_plane_restr0.009116
X-RAY DIFFRACTIONf_dihedral_angle_d5.6062180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.720.2676160.2283383X-RAY DIFFRACTION79
1.72-1.790.2466290.2004444X-RAY DIFFRACTION95
1.79-1.870.2076220.2038477X-RAY DIFFRACTION99
1.87-1.970.2849260.21463X-RAY DIFFRACTION99
1.97-2.090.2533240.2149483X-RAY DIFFRACTION100
2.09-2.250.2881210.2129471X-RAY DIFFRACTION100
2.25-2.480.3298300.2218480X-RAY DIFFRACTION100
2.48-2.840.1637200.2176495X-RAY DIFFRACTION100
2.84-3.570.1687230.1876484X-RAY DIFFRACTION97
3.58-41.680.1737240.1579531X-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