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- PDB-1saq: Crystal Structure of the RNA octamer GIC(GA)GCC -

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Basic information

Entry
Database: PDB / ID: 1saq
TitleCrystal Structure of the RNA octamer GIC(GA)GCC
Components5'-R(*GP*IP*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: 2.7 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*IP*CP*GP*AP*GP*CP*C)-3'
B: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
C: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
D: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
E: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)12,8285
Polymers12,8285
Non-polymers00
Water36020
1
A: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
B: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1312
Polymers5,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'
D: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)5,1312
Polymers5,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: 5'-R(*GP*IP*CP*GP*AP*GP*CP*C)-3'

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


Theoretical massNumber of molelcules
Total (without water)5,1312
Polymers5,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)69.65, 69.65, 67.81
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*IP*CP*GP*AP*GP*CP*C)-3'


Mass: 2565.602 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: 3.9 Å3/Da / Density % sol: 68.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MgCl2, Hepes, PEG400, (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2Hepes11
3PEG40011
4(NH4)2SO411
5MgCl212
6Hepes12
7PEG40012
8(NH4)2SO412

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 3, 1995
RadiationMonochromator: Cu Ka / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 3700 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.7→2.8 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→29.56 Å / σ(F): 2.5 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 339 RANDOM
Rwork0.238 --
all-4991 -
obs-3438 -
Refinement stepCycle: LAST / Resolution: 2.7→29.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 850 0 20 870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.973

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