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- PDB-1agl: STRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1agl
TitleSTRUCTURE OF A DNA-BISDAUNOMYCIN COMPLEX
ComponentsDNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homology4-METHYLBENZYL-N-BIS[DAUNOMYCIN] / DNA
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHu, G.G. / Shui, X. / Leng, F. / Priebe, W. / Chaires, J.B. / Williams, L.D.
CitationJournal: Biochemistry / Year: 1997
Title: Structure of a DNA-bisdaunomycin complex.
Authors: Hu, G.G. / Shui, X. / Leng, F. / Priebe, W. / Chaires, J.B. / Williams, L.D.
History
DepositionMar 25, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Apr 29, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,9682
Polymers1,8091
Non-polymers1,1591
Water1448
1
A: DNA (5'-D(*CP*GP*AP*TP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,9374
Polymers3,6182
Non-polymers2,3182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)28.270, 28.270, 53.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-BDA / 4-METHYLBENZYL-N-BIS[DAUNOMYCIN] / WP631


Mass: 1159.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H66N2O20
#3: 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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5 / Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NA CACODYLATE11
4MGCL211
5SPERMINE_HCL11
6WATER12
7MPD12
Crystal grow
*PLUS
pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.9 mMd(CGATCG)1drop
236 mMsodium cacodylate1drop
32.8 mM1dropMgCl2
45 %MPD1drop
55.7 mMspermine tetrahydrochloride1drop
60.5 mMWP6311drop
730 %1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 1, 1996
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→12 Å / Num. all: 11192 / Num. obs: 2058 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 6.76 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.5
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 12 Å / % possible obs: 93 % / Num. measured all: 11192

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Processing

Software
NameClassification
X-PLORrefinement
ADSCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DDF045

Resolution: 2.2→10 Å / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.314 -10 %RANDOM
Rwork0.199 ---
obs0.199 1061 97.4 %-
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 42 8 170
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_deg3.1
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
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rwork0.285 111 -
obs--82.8 %
Xplor fileSerial no: 1 / Param file: PARDNA.PRO / Topol file: TOPDNA.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3.1

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