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- PDB-6bna: BINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-... -

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Basic information

Entry
Database: PDB / ID: 6bna
TitleBINDING OF AN ANTITUMOR DRUG TO DNA. NETROPSIN AND C-G-C-G-A-A-T-T-BRC-G-C-G
ComponentsDNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(CBR)P*GP*CP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyNETROPSIN / DNA / DNA (> 10)
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.21 Å
AuthorsKopka, M.L. / Yoon, C. / Goodsell, D. / Pjura, P. / Dickerson, R.E.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Binding of an antitumor drug to DNA, Netropsin and C-G-C-G-A-A-T-T-BrC-G-C-G.
Authors: Kopka, M.L. / Yoon, C. / Goodsell, D. / Pjura, P. / Dickerson, R.E.
#1: Journal: Structure and Motion. Membranes, Nucleic Acids and Protein.
Title: The Binding of Netropsin to Double-Helical B-DNA of Sequence C-G-C-G-A-A-T-T-BrC-G-C-G. Single Crystal X-Ray Structure Analysis
Authors: Kopka, M.L. / Pjura, P. / Yoon, C. / Goodsell, D. / Dickerson, R.E.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1985
Title: The Molecular Origin of DNA-Drug Specificity in Netropsin and Distamycin
Authors: Kopka, M.L. / Yoon, C. / Goodsell, D. / Pjura, P. / Dickerson, R.E.
History
DepositionAug 30, 1984Deposition site: BNL / Processing site: BNL
Revision 1.0Oct 29, 1984Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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


Theoretical massNumber of molelcules
Total (without water)7,9153
Polymers7,4852
Non-polymers4301
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.270, 39.620, 63.570
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*TP*TP*(CBR)P*GP*CP*G)-3')


Mass: 3742.288 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Chemical ChemComp-NT / NETROPSIN


Mass: 430.464 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26N10O3 / Comment: antibiotic, antivirus*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: VAPOR DIFFUSION, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3SPERMINE_HCL11
4MG ACETATE11
5WATER12
6MPD12
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.30 mMDNA1drop
20.60 mMnetropsin1drop
30.30 mMspermine hydrochloride1drop
46.30 mMmagnesium acetate1drop
510 %(v/v)MPD1drop
632.5 %1reservoir

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Data collection

DetectorDetector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 3240
Reflection
*PLUS
Highest resolution: 2.2 Å

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Processing

SoftwareName: JACK-LEVITT / Classification: refinement
RefinementResolution: 2.21→8 Å / σ(F): 2 /
RfactorNum. reflection
obs0.211 2528
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.21→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 486 33 75 594
Refinement
*PLUS
Highest resolution: 2.21 Å / Lowest resolution: 8 Å / Num. reflection all: 3140 / σ(F): 2 / Rfactor all: 0.257
Solvent computation
*PLUS
Displacement parameters
*PLUS

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