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- PDB-282d: A CONTINOUS TRANSITION FROM A-DNA TO B-DNA IN THE 1:1 COMPLEX BET... -

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Basic information

Entry
Database: PDB / ID: 282d
TitleA CONTINOUS TRANSITION FROM A-DNA TO B-DNA IN THE 1:1 COMPLEX BETWEEN NOGALAMYCIN AND THE HEXAMER DCCCGGG
ComponentsDNA (5'-D(*CP*CP*CP*GP*GP*G)-3')
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG
Function / homologyNOGALAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCruse, W. / Saludjian, P. / Leroux, Y. / Leger, Y. / El Manouni, D. / Prange, T.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: A continuous transition from A-DNA to B-DNA in the 1:1 complex between nogalamycin and the hexamer dCCCGGG.
Authors: Cruse, W.B. / Saludjian, P. / Leroux, Y. / Leger, G. / Manouni, D.E. / Prange, T.
History
DepositionAug 26, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Oct 23, 1996Provider: repository / Type: Initial release
Revision 1.1May 22, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,4083
Polymers3,6202
Non-polymers7881
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.845, 45.845, 58.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 1810.205 Da / Num. of mol.: 2 / 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.: 47 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3MGCL211
4SPERMINE11
5WATER12
6MPD12
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 38 ℃ / pH: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMhexanucleotide1drop
20.6 mMnogalamycin1drop
32 mM1dropMgCl2
40.3 mMspermine1drop
550 %MPD1reservoir
61

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994 / Details: MULTILAYER MIRROR
RadiationMonochromator: SI(III) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 2492 / % possible obs: 80 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.052 / Rsym value: 0.072 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.18 / % possible all: 45
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å / % possible obs: 80 % / Observed criterion σ(I): 2 / Redundancy: 4.2 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.5 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
AMoREphasing
NUCLSQrefinement
MOSFLMdata reduction
CCP4data reduction
SCALFdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTS FROM DIFFERENT SOURCES: E.G. DDF001, DDF019

Resolution: 2.4→18 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.183 2365 92 %
Displacement parametersBiso mean: 25.7 Å2
Refine Biso
ClassRefine-IDDetailsTreatment
ALL ATOMSX-RAY DIFFRACTIONTRisotropic
ALL WATERSX-RAY DIFFRACTIONTRisotropic
Refinement stepCycle: LAST / Resolution: 2.4→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 240 56 47 343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.011
X-RAY DIFFRACTIONn_angle_d0.023
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it
X-RAY DIFFRACTIONn_sugar_angle_it
X-RAY DIFFRACTIONn_phos_bond_it
X-RAY DIFFRACTIONn_phos_angle_it
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d
X-RAY DIFFRACTIONn_sugar_bond_angle_d
X-RAY DIFFRACTIONn_phos_bond_d0.011
X-RAY DIFFRACTIONn_phos_bond_angle_d0.033
X-RAY DIFFRACTIONn_plane_restr0.036
X-RAY DIFFRACTIONn_chiral_restr0.17
X-RAY DIFFRACTIONn_singtor_nbd0.08
X-RAY DIFFRACTIONn_multtor_nbd0.23
X-RAY DIFFRACTIONn_xhyhbond_nbd0.18
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 18 Å / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_chiral_restr0.17

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