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- PDB-7mky: SARS-CoV-2 frameshifting pseudoknot RNA -

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Basic information

Entry
Database: PDB / ID: 7mky
TitleSARS-CoV-2 frameshifting pseudoknot RNA
ComponentsRNA (66-MER)
KeywordsRNA / Pseudoknot / tetraloop / triple / SARS / virus / COVID / coronavirus / severe acute respiratory syndrome / frameshift
Function / homology: / COBALT HEXAMMINE(III) / RNA / RNA (> 10)
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
CitationJournal: Rna / Year: 2022
Title: Crystal structure of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) frameshifting pseudoknot.
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionApr 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (66-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,95518
Polymers21,2871
Non-polymers66817
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.371, 39.206, 38.803
Angle α, β, γ (deg.)90.000, 97.980, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-395-

HOH

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Components

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RNA chain , 1 types, 1 molecules A

#1: RNA chain RNA (66-MER)


Mass: 21286.672 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 6 types, 282 molecules

#2: Chemical ChemComp-NCO / COBALT HEXAMMINE(III)


Mass: 161.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CoH18N6
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Na
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 34-40% (v/v) MPD, 40 mM sodium cacodylate, pH 5.5, 20 mM magnesium chloride, 1 mM cobalt hexammine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.8266 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.2→38.43 Å / Num. obs: 51812 / % possible obs: 98.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.063 / Net I/σ(I): 8.6 / Num. measured all: 175993 / Scaling rejects: 64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.2-1.222.92.251734025130.1251.5192.7330.496.6
6.57-38.433.60.04111213110.9970.0230.04727.291.8

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LYJ

7lyj


Resolution: 1.31→38.43 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1877 1533 3.85 %
Rwork0.1537 38257 -
obs0.1551 39790 97.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.29 Å2 / Biso mean: 25.1089 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: final / Resolution: 1.31→38.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 1393 24 265 1682
Biso mean--27.96 32.02 -
Num. residues----66
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.31-1.350.2821410.26213527366899
1.35-1.40.24621410.21933535367699
1.4-1.460.22761420.19043512365499
1.46-1.520.22071380.18093465360399
1.52-1.60.19441390.14693483362298
1.6-1.70.17981390.12883461360097
1.7-1.840.17811390.13763476361598
1.84-2.020.19581400.14563484362498
2.02-2.310.2281400.16073479361997
2.31-2.910.22981370.18273425356295
2.91-38.430.13971370.13293410354793

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