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- PDB-418d: 5'-R(*GP*UP*GP*CP*AP*CP*A)-D(P*C)-3' -

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Basic information

Entry
Database: PDB / ID: 418d
Title5'-R(*GP*UP*GP*CP*AP*CP*A)-D(P*C)-3'
ComponentsRNA (5'-R(*GP*UP*GP*CP*AP*CP*AP*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: 2.4 Å
AuthorsMitra, S.N. / Biswas, R. / Shi, K. / Sundaralingam, M.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2000
Title: Crystal structure of an RNA duplex [r(gugcaca)dC]2 with 3'-dinucleoside overhangs forming a superhelix.
Authors: Mitra, S.N. / Biswas, R. / Shi, K. / Sundaralingam, M.
History
DepositionAug 12, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Dec 27, 2023Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,0192
Polymers5,0192
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.290, 45.250, 73.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

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


Mass: 2509.577 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growpH: 7 / Details: pH 7.00

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS
DetectorType: NICOLET / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.4 Å / Num. obs: 1314 / % possible obs: 72.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.042

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
AMoREphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: R(GUAUAUA)DC

Resolution: 2.4→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 126 10 %RANDOM
Rwork0.208 ---
obs0.208 1235 73 %-
all-1235 --
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 332 0 28 360
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.1
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
Xplor fileSerial no: 1 / Param file: PARAM_ND.DNA / Topol file: TOP_NDBX.DNA

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