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- PDB-425d: 5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3' -

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Basic information

Entry
Database: PDB / ID: 425d
Title5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3'
ComponentsDNA (5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3')
KeywordsDNA / DOUBLE HELIX
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural code for DNA recognition revealed in crystal structures of papillomavirus E2-DNA targets.
Authors: Rozenberg, H. / Rabinovich, D. / Frolow, F. / Hegde, R.S. / Shakked, Z.
History
DepositionSep 14, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3')
B: DNA (5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3')


Theoretical massNumber of molelcules
Total (without water)7,3272
Polymers7,3272
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.207, 40.207, 57.575
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Cell settingtetragonal
Space group name H-MP43

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Components

#1: DNA chain DNA (5'-D(*AP*CP*CP*GP*GP*TP*AP*CP*CP*GP*GP*T)-3')


Mass: 3663.392 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.179 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MGCL211
2MNCL211
3SPERMINE11
4SODIUM CACODYLATE11
5MPD11
6SODIUM CACODYLATE12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mg/mlDNA1drop
232 mM1dropMgCl2
33-10 mM1dropMnCl2
47 mMspermine tetrachloride1drop
520 mMsodium cacodylate1drop
65 %(w/v)MPD1drop
718 %1reservoir
8100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 10, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→25.5 Å / Num. all: 2243 / Num. obs: 2243 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.056
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.21 / % possible all: 90.5
Reflection
*PLUS
Num. measured all: 13447
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 86.8 % / Num. unique obs: 2164 / Rmerge(I) obs: 0.21

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Processing

Software
NameVersionClassification
ULTIMAmodel building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: IDEAL B-DNA

Resolution: 2.8→25.5 Å / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflection
Rwork0.219 --
all0.219 2230 -
obs0.219 2230 97.5 %
Refinement stepCycle: LAST / Resolution: 2.8→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 0 8 494
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.9
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: PARAM_NDBX.DNA / Topol file: TOP_NDBX.DNA
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 2230 / σ(F): 0 / Rfactor Rwork: 0.219 / Lowest resolution: 25.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.9
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å

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