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- PDB-1d17: DNA-NOGALAMYCIN INTERACTIONS -

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Basic information

Entry
Database: PDB / ID: 1d17
TitleDNA-NOGALAMYCIN INTERACTIONS
ComponentsDNA (5'-D(*(5CM)P*GP*TP*AP*(5CM)P*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyNOGALAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsEgli, M. / Williams, L.D. / Frederick, C.A. / Rich, A.
Citation
Journal: Biochemistry / Year: 1991
Title: DNA-nogalamycin interactions.
Authors: Egli, M. / Williams, L.D. / Frederick, C.A. / Rich, A.
History
DepositionAug 8, 1990Deposition site: BNL / Processing site: BNL
Revision 1.0Jul 15, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 24, 2011Group: Atomic model / Derived calculations
Revision 1.4Feb 7, 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(*(5CM)P*GP*TP*AP*(5CM)P*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,6252
Polymers1,8371
Non-polymers7881
Water70339
1
A: DNA (5'-D(*(5CM)P*GP*TP*AP*(5CM)P*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,2504
Polymers3,6752
Non-polymers1,5762
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)26.300, 26.300, 100.010
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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


Mass: 1837.271 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NGM / NOGALAMYCIN


Mass: 787.803 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H49NO16 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, SITTING DROP / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3METHANOL11
4NA CACODYLATE11
5MGCL211
6SPERMINE11
7WATER12
8MPD12
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, sitting drop
Details: Williams, L.D., (1990) Proc.Natl.Acad.Sci.USA, 87, 2225.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.5 mMDNA1dropsingle stranded
240 mMsodium cacodylate1droppH6.0
34 mMspermine1drop
413 mM1dropMgCl2
58 %MPD1drop
65 %satmethanol1dropwith nogalamycin
730 %MPD1reservoir
81

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU AFC-5 / Detector: DIFFRACTOMETER
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementHighest resolution: 2 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.206 -
obs0.206 809
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 122 56 39 217
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Highest resolution: 2 Å / Lowest resolution: 2.5 Å / Num. reflection obs: 809 / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_angle_deg
X-RAY DIFFRACTIONn_dihedral_angle_d
X-RAY DIFFRACTIONn_improper_angle_d
X-RAY DIFFRACTIONn_mcbond_it
X-RAY DIFFRACTIONn_scbond_it
X-RAY DIFFRACTIONn_mcangle_it
X-RAY DIFFRACTIONn_scangle_it

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