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- PDB-1evp: CRYSTAL STRUCTURE OF THE CHIMERICAL DECAMER D(CCACTAGTG)R(G) -

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Basic information

Entry
Database: PDB / ID: 1evp
TitleCRYSTAL STRUCTURE OF THE CHIMERICAL DECAMER D(CCACTAGTG)R(G)
ComponentsDNA/RNA (5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP)-R(*G)-3')
KeywordsDNA-RNA HYBRID / A-DNA / B-DNA / DNA-RNA CHIMERA / NUCLEIC ACID STRUCTURE / STRUCTURAL CONVERSION / DNA-RNA COMPLEX
Function / homologyDNA/RNA hybrid
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsWahl, M.C. / Sundaralingam, M.
CitationJournal: Nucleic Acids Res. / Year: 2000
Title: B-form to A-form conversion by a 3'-terminal ribose: crystal structure of the chimera d(CCACTAGTG)r(G).
Authors: Wahl, M.C. / Sundaralingam, M.
History
DepositionApr 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 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
Q: DNA/RNA (5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP)-R(*G)-3')
R: DNA/RNA (5'-D(*CP*CP*AP*CP*TP*AP*GP*TP*GP)-R(*G)-3')


Theoretical massNumber of molelcules
Total (without water)6,1222
Polymers6,1222
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)23.90, 45.76, 49.27
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

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


Mass: 3061.005 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MGCL2, SPERMINE, MPD, SODIUM CACODYLATE, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2SPERMINE11
3SODIUM CACODYLATE11
4MPD11
5MPD12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMoligomer1drop
250 mMspermine tetrachloride1drop
35 mM1dropMgCl2
420 mMNa cacodylate1drop
510 %1drop
660 %MPD1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR / Date: Jul 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 4634 / Num. obs: 4634 / % possible obs: 87.4 % / Rmerge(I) obs: 0.031
Reflection shellResolution: 1.8→1.9 Å / % possible all: 67.2
Reflection shell
*PLUS
% possible obs: 67.2 %

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 1.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.228 464 10 %RANDOM
Rwork0.166 ---
obs0.166 ---
all-4634 --
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 406 0 77 483
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_deg2.5
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg31.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.9

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