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- PDB-1sm5: Crystal Structure of a DNA Decamer Containing a Thymine-dimer -

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Basic information

Entry
Database: PDB / ID: 1sm5
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*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3'
KeywordsDNA / UV-damaged DNA / Thymine dimer / DNA decamer
Function / homologyDNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 Thymine-dimer
Authors: Park, H. / Zhang, K. / Ren, Y. / Nadji, S. / Sinha, N. / Taylor, J.-S. / Kang, C.
History
DepositionMar 8, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionMay 25, 2004ID: 1MV7
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)12,4364
Polymers12,4364
Non-polymers00
Water93752
1
A: 5'-D(*GP*CP*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3'
B: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2182
Polymers6,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(*GP*CP*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3'
D: 5'-D(*CP*GP*AP*AP*TP*TP*AP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)6,2182
Polymers6,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.5, 53.85, 75.33
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*(BRU)P*TP*AP*AP*TP*(BRU)P*CP*G)-3'


Mass: 3164.742 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.: 52 / 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: 1.93 Å3/Da / Density % sol: 36.22 %
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
5PEG 40012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9205, 0.8434, 0.9207
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2001 / Details: double crystal monochromator
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92051
20.84341
30.92071
ReflectionResolution: 1.9→50 Å / Num. all: 79490 / Num. obs: 7865 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MAD / Resolution: 2→10 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 372 5 %RANDOM
Rwork0.198 ---
all-6819 --
obs-6447 --
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 808 0 52 860
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.35
X-RAY DIFFRACTIONx_bond_d0.023

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