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- PDB-377d: 5'-R(*CP*GP*UP*AP*CP*DG)-3' -

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Basic information

Entry
Database: PDB / ID: 377d
Title5'-R(*CP*GP*UP*AP*CP*DG)-3'
ComponentsRNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
KeywordsRNA / A-RNA / DOUBLE HELIX
Function / homologyRNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsBiswas, R. / Mitra, S.N. / Sundaralingam, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1998
Title: 1.76 A structure of a pyrimidine start alternating A-RNA hexamer r(CGUAC)dG.
Authors: Biswas, R. / Mitra, S.N. / Sundaralingam, M.
History
DepositionJan 26, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Aug 10, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Feb 21, 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-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
B: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
C: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
D: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)7,5014
Polymers7,5014
Non-polymers00
Water1,53185
1
A: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
B: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)3,7502
Polymers3,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-0.9 kcal/mol
Surface area2370 Å2
MethodPISA
2
C: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')
D: RNA-DNA (5'-R(*CP*GP*UP*AP*CP*DG)-3')


Theoretical massNumber of molelcules
Total (without water)3,7502
Polymers3,7502
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-0.4 kcal/mol
Surface area2380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.530, 44.610, 94.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 1875.189 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal grow
*PLUS
Temperature: 291 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 mMRNA1dropsingle strand concentration
22.5 mMmagnesium acetate1drop
30.5 mMspermine1drop
410 mMsodium cacodylate1drop
50.2 mMDMA1drop
650 %MPD1reservoir

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU R-AXIS II
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 8 Å / Num. obs: 4757 / % possible obs: 76 % / Rmerge(I) obs: 0.067 / Rmerge F obs: 2
Reflection shell
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 2 Å / % possible obs: 65 %

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Processing

Software
NameClassification
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
RefinementResolution: 1.76→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.232 -
Rwork0.188 -
obs0.188 4757
Refinement stepCycle: LAST / Resolution: 1.76→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 496 0 85 581
Xplor fileSerial no: 1 / Param file: PARAM_ND.DNA / Topol file: TOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 8 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4

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