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- PDB-394d: CRYSTAL STRUCTURE OF TWO SELF-COMPLEMENTARY CHIMERIC DECAMERS D(C... -

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Basic information

Entry
Database: PDB / ID: 394d
TitleCRYSTAL STRUCTURE OF TWO SELF-COMPLEMENTARY CHIMERIC DECAMERS D(CCGG)R(C)D(GCCGG) AND D(CCGG)R(CG)D(CCGG)
ComponentsDNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP*GP)-D(*CP*CP*GP*G)-3')
KeywordsDNA-RNA HYBRID / A-DNA/RNA / DOUBLE HELIX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsBan, C. / Sundaralingam, M.
CitationJournal: To be Published
Title: Crystal Structure of Two Self-Complementary Chimeric Decamers d(CCGG)r(C)d(GCCGG) and d(CCGG)r(CG)d(CCGG)
Authors: Ban, C. / Ramakrishnan, B. / Sundaralingam, M.
History
DepositionApr 29, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0May 1, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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: DNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP*GP)-D(*CP*CP*GP*G)-3')
B: DNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP*GP)-D(*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1582
Polymers6,1582
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)25.650, 45.530, 47.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA/RNA hybrid DNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP*GP)-D(*CP*CP*GP*G)-3')


Mass: 3078.980 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA-CACODYLATE11
3COBALT HEXAMINE11
4MPD11
5WATER12
6MPD12

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Data collection

DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 23, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 3970 / % possible obs: 96 % / Redundancy: 4 % / Rmerge(I) obs: 0.025

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.2refinement
XENGENdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.177 -
obs0.177 3757
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 408 0 62 470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: PARAM11.DNA

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