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- PDB-393d: CRYSTAL STRUCTURE OF TWO SELF-COMPLEMENTARY CHIMERIC DECAMER D(CC... -

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Basic information

Entry
Database: PDB / ID: 393d
TitleCRYSTAL STRUCTURE OF TWO SELF-COMPLEMENTARY CHIMERIC DECAMER D(CCGG)R(C)D(GCCGG) AND D(CCGG)R(CG)D(CCGG)
ComponentsDNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP)-D(*GP*CP*CP*GP*G)-3')
KeywordsDNA/RNA / A-T-RNA / DOUBLE HELIX / DNA-RNA COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBan, C. / Sundaralingam, M. / Ramakrishnan, B.
CitationJournal: To be Published
Title: Crystal Structure of Two Self-Complementary Chimeric Decamer 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 1.3Dec 14, 2016Group: Structure summary
Revision 1.4Feb 1, 2017Group: Database references
Revision 1.5May 3, 2017Group: Source and taxonomy / Structure summary
Revision 1.6Feb 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

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP)-D(*GP*CP*CP*GP*G)-3')
B: DNA/RNA (5'-D(*CP*CP*GP*GP)-R(*CP)-D(*GP*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1262
Polymers6,1262
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.520, 44.850, 47.580
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)-D(*GP*CP*CP*GP*G)-3')


Mass: 3062.980 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
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
4WATER12
5MPD12

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Data collection

DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jun 13, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 3219 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.049

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLOR3.2refinement
XENGENdata scaling
RefinementResolution: 2→8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.181 -
obs-2902
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 406 0 70 476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.8
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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