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- PDB-3mja: Cricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate, ... -

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Basic information

Entry
Database: PDB / ID: 3mja
TitleCricket Paralysis Virus IGR IRES Domain 3 RNA bound to selenate, structure #2
Components
  • Domain 3 of the cricket paralysis virus intergenic region IRES RNA
  • RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')
KeywordsRNA / RNA psuedoknot / anions / selenate
Function / homologySELENATE ION / RNA / RNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKieft, J.S. / Golden, B.L. / Costantino, D.A. / Chase, E.
CitationJournal: Rna / Year: 2010
Title: Identification and characterization of anion binding sites in RNA.
Authors: Kieft, J.S. / Chase, E. / Costantino, D.A. / Golden, B.L.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Domain 3 of the cricket paralysis virus intergenic region IRES RNA
C: RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3156
Polymers13,7432
Non-polymers5724
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.250, 59.250, 99.775
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: RNA chain Domain 3 of the cricket paralysis virus intergenic region IRES RNA


Mass: 9326.556 Da / Num. of mol.: 1 / Fragment: Domain 3 RNA / Mutation: U6178A / Source method: obtained synthetically / Details: In vitro transcription
#2: RNA chain RNA (5'-R(P*UP*AP*AP*GP*AP*AP*AP*UP*UP*UP*AP*CP*CP*U)-3')


Mass: 4416.675 Da / Num. of mol.: 1 / Fragment: Domain 3 RNA / Mutation: A6199G / Source method: obtained synthetically
#3: Chemical
ChemComp-SE4 / SELENATE ION


Mass: 142.958 Da / Num. of mol.: 4 / Fragment: Domain 3 RNA / Mutation: U6198U / Source method: obtained synthetically / Formula: O4Se

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 1.8 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH; moved to 2.4 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 ...Details: 1.8 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH; moved to 2.4 M lithium selenate, 42.5 mM magnesium chloride, 0.5 mM spermidine, 10 mM HEPES-KOH, 50 mM HEPES-NaOH (all otherfor cryoprotections, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.9786 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.8→42 Å / Num. obs: 8365 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3B31

3b31


Resolution: 2.8→30 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 818 9.8 %RANDOM
Rwork0.233 ---
obs-6953 99.9 %-
Solvent computationBsol: 35 Å2
Displacement parametersBiso max: 100.92 Å2 / Biso mean: 47.745 Å2 / Biso min: 27.36 Å2
Baniso -1Baniso -2Baniso -3
1--6.24 Å20 Å20 Å2
2--2.302 Å20 Å2
3---3.937 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 917 20 0 937
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.381
X-RAY DIFFRACTIONc_mcbond_it1.5591.5
X-RAY DIFFRACTIONc_mcangle_it2.5122
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5CNS_TOPPAR:irhex.paramCNS_TOPPAR:irhex.top

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