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- PDB-402d: 5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3' -

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Basic information

Entry
Database: PDB / ID: 402d
Title5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3'
ComponentsRNA(5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3')
KeywordsRNA / RNA DOUBLE HELIX / RNA WITH TANDEM C-A+ BASE PAIR
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsJang, S.B. / Hung, L.-W. / Chi, Y.-I. / Holbrook, E.L. / Carter, R. / Holbrook, S.R.
CitationJournal: Biochemistry / Year: 1998
Title: Structure of an RNA internal loop consisting of tandem C-A+ base pairs.
Authors: Jang, S.B. / Hung, L.W. / Chi, Y.I. / Holbrook, E.L. / Carter, R.J. / Holbrook, S.R.
History
DepositionJun 4, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 16, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA(5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3')
B: RNA(5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)5,0812
Polymers5,0812
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.737, 42.737, 123.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: RNA chain RNA(5'-R(*CP*GP*CP*CP*AP*GP*CP*G)-3')


Mass: 2540.593 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5 / Details: pH 5.50, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NACL11
3MGCL211
4SPERMINE TETRAHYDROCHLORIDE11
5PRECIPITATING SOLUTION11
6MPD12
7NA CACODYLATE12
Crystal
*PLUS
Density % sol: 42.7 %
Crystal grow
*PLUS
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12 mMRNA1drop
220 mM1reservoirNaCl
35 mM1reservoirMgCl2
42 mMspermine tetrahydrochloride1reservoir
535 %MPD1reservoir
6100 mMsodium cacodylate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 2101 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % possible obs: 96.8 % / Num. measured all: 25094
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 80.2 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.3→8 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 10000 / Isotropic thermal model: ISOTROPIC / σ(F): 2.5
RfactorNum. reflection% reflection
Rfree0.263 146 7.1 %
Rwork0.207 --
obs0.207 1695 83 %
all-1695 -
Solvent computationSolvent model: BULK SOLVENT / Bsol: 57.1 Å2 / ksol: 0.45 e/Å3
Refine Biso Class: 1
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 336 0 30 366
Xplor fileSerial no: 1 / Param file: DNA_RNA_REP.PARAM WATER_R
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / σ(F): 2.5 / % reflection Rfree: 10 % / Num. reflection obs: 2030
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.035
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg0.867

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