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- PDB-1d93: STRUCTURAL VARIATION IN D(CTCTAGAG). IMPLICATIONS FOR PROTEIN-DNA... -

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Basic information

Entry
Database: PDB / ID: 1d93
TitleSTRUCTURAL VARIATION IN D(CTCTAGAG). IMPLICATIONS FOR PROTEIN-DNA INTERACTIONS
ComponentsDNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')
KeywordsDNA / A-DNA / DOUBLE HELIX
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.15 Å
AuthorsHunter, W.N. / Langlois D'Estaintot, B. / Kennard, O.
CitationJournal: Biochemistry / Year: 1989
Title: Structural variation in d(CTCTAGAG). Implications for protein-DNA interactions.
Authors: Hunter, W.N. / D'Estaintot, B.L. / Kennard, O.
History
DepositionOct 17, 1992Deposition site: BNL / Processing site: NDB
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
A: DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)2,4271
Polymers2,4271
Non-polymers00
Water63135
1
A: DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')

A: DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)4,8532
Polymers4,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)42.520, 42.520, 24.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain DNA (5'-D(*CP*TP*CP*TP*AP*GP*AP*G)-3')


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 291.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 6.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mloctamer1drop
260 mMsodium cacodylate1drop
325 mMmagnesium chloride1drop
41 mMspermine hydrochloride1drop
57 %(v/v)MPD1drop
650 %(v/v)MPD1reservoir
71

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Data collection

DetectorType: SYNTEX P21 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.15 Å / Num. all: 2320 / Num. obs: 1378
Reflection
*PLUS
Highest resolution: 2.15 Å / % possible obs: 70 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.075

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.15→8 Å / σ(I): 1 /
RfactorNum. reflection
obs0.147 931
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 161 0 35 196
Refinement
*PLUS
Highest resolution: 2.15 Å / Lowest resolution: 8 Å / Num. reflection obs: 931 / σ(I): 1 / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS

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