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- PDB-1n4e: Crystal Structure of a DNA Decamer Containing a Thymine-dimer -

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Basic information

Entry
Database: PDB / ID: 1n4e
TitleCrystal Structure of a DNA Decamer Containing a Thymine-dimer
Components
  • 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'
  • 5'-D(*GP*CP*TP*TP*AP*AP*TP*TP*CP*G)-3'
KeywordsDNA / UV-damaged DNA / Thymine dimer / DNA decamer
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPark, H. / Zhang, K. / Ren, Y. / Nadji, S. / Sinha, N. / Taylor, J.-S. / Kang, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Crystal structure of a DNA decamer containing a cis-syn thymine dimer.
Authors: Park, H. / Zhang, K. / Ren, Y. / Nadji, S. / Sinha, N. / Taylor, J.S. / Kang, C.
History
DepositionOct 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*GP*CP*TP*TP*AP*AP*TP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'
C: 5'-D(*GP*CP*TP*TP*AP*AP*TP*TP*CP*G)-3'
D: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)12,1764
Polymers12,1764
Non-polymers00
Water1,00956
1
A: 5'-D(*GP*CP*TP*TP*AP*AP*TP*TP*CP*G)-3'
B: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*TP*TP*AP*AP*TP*TP*CP*G)-3'
D: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,0882
Polymers6,0882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)21.11, 54.01, 74.19
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 3035.003 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Mass: 3053.031 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: MgCl2, HEPES-Na, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Components of the solutions
IDNameCrystal-IDSol-ID
1MgCl211
2HEPES-Na11
3PEG 40011
4MgCl212
Crystal grow
*PLUS
Temperature: 4 and 20 ℃ / pH: 8 / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMDNA1drop
210 mMTris-HCl1droppH8.0
31 mMEDTA1drop
40.2 M1reservoirMgCl2
50.1 Msodium HEPES1reservoirpH7.5
630 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: mirror
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 5775 / Num. obs: 4616 / % possible obs: 88.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.39 Å / % possible all: 76.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 10325 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 76.4 % / Rmerge(I) obs: 0.198

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Cross valid method: random / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.255 159 5 %
Rwork0.197 --
all-3220 -
obs-3061 -
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 0 56 864
LS refinement shellResolution: 2.5→2.61 Å /
RfactorNum. reflection
Rfree0.302 14
Rwork0.252 -
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.034
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.3021

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