[English] 日本語
Yorodumi
- PDB-5ay3: Crystal structure of RNA duplex containing C-C base pairs -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ay3
TitleCrystal structure of RNA duplex containing C-C base pairs
ComponentsRNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')
KeywordsRNA / X-Ray analysis / metallo base pair / Ag(I)
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsKondo, J. / Tada, Y. / Dairaku, T. / Saneyoshi, H. / Okamoto, I. / Tanaka, Y. / Ono, A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Authors: Kondo, J. / Tada, Y. / Dairaku, T. / Saneyoshi, H. / Okamoto, I. / Tanaka, Y. / Ono, A.
History
DepositionAug 6, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source ...citation / diffrn_source / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.3Mar 20, 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: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')
B: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)7,7002
Polymers7,7002
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-0 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.160, 44.460, 27.370
Angle α, β, γ (deg.)90.00, 109.43, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: RNA chain RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3')


Mass: 3850.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: MPD, Spermine, Lithium Nitrate, MOPS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
1.41.44179410.243
1.441.48165510.192
1.481.52169410.151
1.521.57159410.12
1.571.62157310.093
1.621.67154410.063
1.671.74143010.053
1.741.81145710.052
1.811.89130010.044
1.891.98132210.04
1.982.09126410.036
2.092.22111710.034
2.222.37109210.032
2.372.5699310.03
2.562.892710.028
2.83.1384610.022
3.133.6272310.022
3.624.4363210.02
4.436.2750110.023
6.2725.825410.021
ReflectionResolution: 1.2→25.8 Å / Num. obs: 19127 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 17.18 Å2 / Net I/σ(I): 22.16
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.2-1.2330.9620.1885.414234142714050.22798.5
1.23-1.270.9750.1616.64274136213550.19499.5
1.27-1.30.9780.1527.014478138413740.18299.3
1.3-1.340.9810.1298.384231128612850.15499.9
1.34-1.390.9860.119.523986125612480.13399.4
1.39-1.440.9910.08711.934074125512470.10499.4
1.44-1.490.9930.07214.253800117211650.08699.4
1.49-1.550.9950.05717.343641110410990.06899.5
1.55-1.620.9970.04820.423470108810900.057100
1.62-1.70.9990.03526.163595107410620.04198.9
1.7-1.790.9980.03229.7331119759730.03999.8
1.79-1.90.9980.03132.5732449539490.03799.6
1.9-2.030.9980.02736.1428858798750.03399.5
2.03-2.190.9990.02738.8527238258180.03299.2
2.19-2.40.9990.02541.4724197577480.0398.8
2.4-2.690.9990.02345.3323106986850.02798.1
2.69-3.10.9990.0248.4619616196110.02598.7
3.1-3.80.9990.01852.4116835105040.02298.8
3.8-5.370.9990.01953.1913224084040.02299
5.37-25.80.9980.0250.647182352300.02497.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
CNS1.3refinement
XSCALEdata scaling
PHENIXphasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.2→25.8 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.1985 1891 9.8 %
Rwork0.1841 17236 -
obs-19127 99.2 %
Solvent computationBsol: 43.3617 Å2
Displacement parametersBiso max: 60.77 Å2 / Biso mean: 16.3542 Å2 / Biso min: 7.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.417 Å20 Å2-2.148 Å2
2---1.415 Å20 Å2
3---1.833 Å2
Refinement stepCycle: LAST / Resolution: 1.2→25.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 500 40 171 711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_scbond_it1.1192
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scangle_it1.5462.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.240.27291900.24871682187296.3
1.24-1.290.27421750.24881717189299.6
1.29-1.350.27791790.25041733191299.7
1.35-1.420.25652110.22861686189799.6
1.42-1.510.21682130.20921714192799.5
1.51-1.630.20741840.18921738192299.8
1.63-1.790.19911560.17591749190599.7
1.79-2.050.19951660.17681747191399.7
2.05-2.590.20612250.19371703192899
2.59-1000.16061920.15591767195999.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1bru.param
X-RAY DIFFRACTION2dna-rna_free.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

+
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