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- PDB-386d: THREE-DIMENSIONAL STRUCTURE AND REACTIVITY OF A PHOTOCHEMICAL CLE... -

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Basic information

Entry
Database: PDB / ID: 386d
TitleTHREE-DIMENSIONAL STRUCTURE AND REACTIVITY OF A PHOTOCHEMICAL CLEAVAGE AGENT BOUND TO DNA
ComponentsDNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyN,N-BIS(3-AMINOPROPYL)-2-ANTHRAQUINONESULFONAMIDE / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGasper, S.M. / Armitage, B. / Shui, X. / Hu, G.G. / Yu, C. / Schuster, G. / Williams, L.D.
CitationJournal: J.Am.Chem.Soc. / Year: 1998
Title: Three-Dimensional Structure and Reactivity of a Photochemical Cleavage Agent Bound to DNA
Authors: Gasper, S.M. / Armitage, B. / Shui, X. / Hu, G.G. / Yu, C. / Schuster, G. / Williams, L.D.
History
DepositionMar 11, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Mar 12, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Feb 21, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,2132
Polymers1,8091
Non-polymers4031
Water39622
1
A: DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,4254
Polymers3,6182
Non-polymers8072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)31.020, 31.020, 64.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-21-

HOH

21A-22-

HOH

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-AQS / N,N-BIS(3-AMINOPROPYL)-2-ANTHRAQUINONESULFONAMIDE


Mass: 403.495 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N3O4S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2NA CACODYLATE11
3MGCL211
4MPD11
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.8 Mprotein1drop
221 Msodium cacodylate1drop
33.3 mM1dropMgCl2
41.1 %1drop
50.8 mMspermine trihydrochloride1drop
61.5 mMAQS21drop
710 %1reservoir

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Data collection

DiffractionMean temperature: 136 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 12.44 % / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.8→1.88 Å / % possible all: 65.6
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 1972 / Num. measured all: 24530

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Processing

Software
NameVersionClassification
MADmodel building
X-PLOR3.1refinement
ADSCdata collection
MADphasing
RefinementResolution: 1.8→10 Å / σ(F): 5
RfactorNum. reflection
Rfree0.268 -
Rwork0.196 -
obs0.196 1680
all-1972
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 28 22 170
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.02
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 5 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.025
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Num. reflection obs: 145 / Rfactor obs: 0.302

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