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- PDB-414d: 5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3' -

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Basic information

Entry
Database: PDB / ID: 414d
Title5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3'
ComponentsDNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSavitha, G. / Viswamitra, M.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: An A-DNA structure with two independent duplexes in the asymmetric unit.
Authors: Savitha, G. / Viswamitra, M.A.
History
DepositionJul 13, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Jun 14, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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 (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
C: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)12,1884
Polymers12,1884
Non-polymers00
Water2,090116
1
A: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
B: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')
D: DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')


Theoretical massNumber of molelcules
Total (without water)6,0942
Polymers6,0942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.504, 46.084, 28.465
Angle α, β, γ (deg.)90.00, 100.74, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: DNA chain
DNA (5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3')


Mass: 3046.980 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.29 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
5MPD12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 291 K / pH: 6.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMDNA1drop
220 mMsodium cacodylate1drop
330 mM1dropMgCl2
42 mMspermine tetrachloride1drop
55 %1drop
650 %MPD1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12911
21
31
41
Diffraction source
SourceTypeID
ROTATING ANODERIGAKU1
2
3
4
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEDec 15, 1996
2
3
4
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDRelative weight
11
21
31
41
ReflectionResolution: 1.8→10 Å / Num. all: 10033 / Num. obs: 10033 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Num. measured all: 41278

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MARdata reduction
XDSdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 1 /
Num. reflection% reflection
obs3583 94 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 0 116 924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
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_deg1.56
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
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 1 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg32.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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