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- PDB-419d: OCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRIC... -

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Basic information

Entry
Database: PDB / ID: 419d
TitleOCTAMER 5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3' WITH SIX WATSON-CRICK BASE-PAIRS AND TWO 3' OVERHANG RESIDUES
ComponentsDNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
KeywordsDNA-RNA HYBRID / HIGHLY BENT RNA / SUPERHELICES / DNA-RNA COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMitra, S.M. / Shi, K. / Biswas, R. / Sundaralingam, M.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The crystal structure of the octamer [r(guauaca)dC]2 with six Watson-Crick base-pairs and two 3' overhang residues.
Authors: Shi, K. / Biswas, R. / Mitra, S.N. / Sundaralingam, M.
History
DepositionAug 12, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0May 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
B: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
C: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
D: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')


Theoretical massNumber of molelcules
Total (without water)9,9784
Polymers9,9784
Non-polymers00
Water1,13563
1
A: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
B: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9892
Polymers4,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')
D: DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')


Theoretical massNumber of molelcules
Total (without water)4,9892
Polymers4,9892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.190, 45.530, 74.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid
DNA/RNA (5'-R(*GP*UP*AP*UP*AP*CP*A)-D(P*C)-3')


Mass: 2494.561 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11 mMRNA1dropsingle stranded conc.
250 mMsodium cacodylate1drop
310 mM1dropMgCl2
425 mMspermine tetrachloride1drop
52.4 %(v/v)MPD1drop
640 %MPD1reservoir

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→14.7 Å / Num. obs: 3661 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.037
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. obs: 3592 / % possible obs: 83.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R(GUGCACA)DC

Resolution: 2.2→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.278 365 10 %RANDOM
Rwork0.186 ---
obs0.186 3592 81.5 %-
all-3592 --
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 660 0 63 723
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d14.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.19
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg12.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

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