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- PDB-1ndn: MOLECULAR STRUCTURE OF NICKED DNA. MODEL T4 -

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Basic information

Entry
Database: PDB / ID: 1ndn
TitleMOLECULAR STRUCTURE OF NICKED DNA. MODEL T4
Components
  • DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')
  • DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / NICKED
Function / homologyDNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAymani, J. / Coll, M. / Van Der Marel, G.A. / Van Boom, J.H. / Wang, A.H.-J. / Rich, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1990
Title: Molecular structure of nicked DNA: a substrate for DNA repair enzymes.
Authors: Aymami, J. / Coll, M. / van der Marel, G.A. / van Boom, J.H. / Wang, A.H. / Rich, A.
#1: Journal: Biochemistry / Year: 1989
Title: Molecular Structure of the Netropsin-d(CGCGATATCGCG) Complex. DNA Conformation in an Alternating AT Segment
Authors: Coll, M. / Aymami, J. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. / Wang, A.H.-J.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987
Title: A Bifurcated Hydrogen-Bonded Conformation in the d(*A(dot)*T) Base Pairs of the DNA Dodecamer d(CGCAAATTTGCG) and Its Complex With Distamycin
Authors: Coll, M. / Frederick, C.A. / Wang, A.H.-J. / Rich, A.
#3: Journal: Nature / Year: 1980
Title: Crystal Structure Analysis of a Complete Turn of B-DNA
Authors: Wing, R. / Drew, H. / Takano, T. / Broka, C. / Tanaka, S. / Itakura, K. / Dickerson, R.E.
History
DepositionJan 15, 1992Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 14, 1992Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')
B: DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')
C: DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')


Theoretical massNumber of molelcules
Total (without water)7,2823
Polymers7,2823
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-5 kcal/mol
Surface area4310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.990, 44.030, 66.620
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 chain DNA (5'-D(*CP*GP*CP*GP*AP*AP*AP*AP*CP*GP*CP*G)-3')


Mass: 3681.420 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*GP*CP*GP*TP*T)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*TP*TP*CP*GP*CP*G)-3')


Mass: 1800.203 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5 / Details: pH 5.00, VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4NA CACODYLATE11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDChemical formulaSol-ID
10.5 mMoligonucleotide1
22.9 mM1MgCl2
329 mMsodium cacodylate1
48.6 mMspermine-4HCL1
51.9 mMHoechest332581
62 %MPD11
750 %1

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 3 Å / Num. obs: 553 / Observed criterion σ(F): 2
Reflection
*PLUS
Highest resolution: 3 Å / Observed criterion σ(F): 2

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Processing

Software
NameClassification
ULTIMAmodel building
NUCLSQrefinement
ULTIMAphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 3 Å / σ(F): 2 /
RfactorNum. reflection
obs0.186 553
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 483 0 61 544

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