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- PDB-1sa9: Crystal Structure of the RNA octamer GGCGAGCC -

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Basic information

Entry
Database: PDB / ID: 1sa9
TitleCrystal Structure of the RNA octamer GGCGAGCC
Components5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
KeywordsRNA / RNA double helix / RNA tandem G-A base pair
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.86 Å
AuthorsJang, S.B. / Baeyens, K. / Jeong, M.S. / SantaLucia Jr, J. / Turner, D. / Holbrook, S.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structures of two RNA octamers containing tandem G.A base pairs.
Authors: Jang, S.B. / Baeyens, K. / Jeong, M.S. / SantaLucia, J. / Turner, D. / Holbrook, S.R.
History
DepositionFeb 9, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 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: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
B: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
C: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
E: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)12,9035
Polymers12,9035
Non-polymers00
Water36020
1
A: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
B: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1612
Polymers5,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'
D: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1612
Polymers5,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'

E: 5'-R(*GP*GP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1612
Polymers5,1612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)69.65, 69.65, 68.36
Angle α, β, γ (deg.)90, 90, 120
Int Tables number172
Space group name H-MP64

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Components

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


Mass: 2580.617 Da / Num. of mol.: 5 / Source method: obtained synthetically / Details: RNA double helix
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.91 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate, PEG8000, Zn(acetate)2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1sodium cacodylate11
2PEG800011
3Zn(acetate)211
4sodium cacodylate12
5PEG800012
6Zn(acetate)212

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 3, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→60.32 Å
Reflection shellResolution: 2.8→2.9 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.86→60.32 Å / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.255 -RANDOM
Rwork0.241 --
all-4495 -
obs-3273 -
Refinement stepCycle: LAST / Resolution: 2.86→60.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 855 0 20 875
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.074

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