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- PDB-277d: SUBSTITUTIONS AT C2' OF DAUNOSAMINE IN THE ANTICANCER DAUNORUBICI... -

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Basic information

Entry
Database: PDB / ID: 277d
TitleSUBSTITUTIONS AT C2' OF DAUNOSAMINE IN THE ANTICANCER DAUNORUBICIN ALTER ITS DNA-BINDING SEQUENCE SPECIFICITY
Components5'-D(*CP*GP*CP*(G49)P*CP*G)-3'
KeywordsDNA / RIGHT HANDED DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homology2'-BROMO-4'-EPIDAUNORUBICIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsGao, Y.-G. / Priebe, W. / Wang, A.H.-J.
CitationJournal: Eur.J.Biochem. / Year: 1996
Title: Substitutions at C2' of daunosamine in the anticancer drug daunorubicin alter its DNA-binding sequence specificity.
Authors: Gao, Y.G. / Priebe, W. / Wang, A.H.
History
DepositionJul 22, 1996Deposition site: NDB / Processing site: NDB
Revision 1.0Sep 16, 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_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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 5'-D(*CP*GP*CP*(G49)P*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,4312
Polymers1,8241
Non-polymers6061
Water79344
1
A: 5'-D(*CP*GP*CP*(G49)P*CP*G)-3'
hetero molecules

A: 5'-D(*CP*GP*CP*(G49)P*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8614
Polymers3,6482
Non-polymers1,2132
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)28.190, 28.190, 52.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: DNA chain 5'-D(*CP*GP*CP*(G49)P*CP*G)-3'


Mass: 1824.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-DM8 / 2'-BROMO-4'-EPIDAUNORUBICIN / WP401 / DAUNOMYCIN DERIVATIVE / DAUNORUBICIN DERIVATIVE


Mass: 606.416 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28BrNO10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6 / Details: pH 6.00, VAPOR DIFFUSION, temperature 298.00K / Temp details: ROOM TEMPERATURE
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3BACL211
4NA CACODYLATE11
5SPERMINE11
6WATER12
7MPD12
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.2 mMsingle-stranded DNA hexamer1drop
24 mM1dropBaCl2
335 mMsodium cacodylate1drop
42.5 mMspermine1drop
51.2 mMdrug1drop
65 %MPD1drop
740 %1reservoir
88 mM1dropHCHO
91 %1reservoirHCHO

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 19, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 4 % / Rmerge(I) obs: 0.069
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Redundancy: 4 %
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / % possible obs: 75.4 %

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Processing

Software
NameClassification
MSCdata collection
NUCLSQrefinement
MSCdata reduction
RefinementResolution: 1.8→10 Å / σ(F): 4 /
RfactorNum. reflection
obs0.213 1667
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 120 40 44 204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.023
X-RAY DIFFRACTIONn_angle_d
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_d
X-RAY DIFFRACTIONn_phos_bond_angle_d
X-RAY DIFFRACTIONn_plane_restr
X-RAY DIFFRACTIONn_chiral_restr
X-RAY DIFFRACTIONn_singtor_nbd
X-RAY DIFFRACTIONn_multtor_nbd
X-RAY DIFFRACTIONn_xhyhbond_nbd
Software
*PLUS
Name: NUCLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / σ(F): 4
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONn_bond_d0.023
X-RAY DIFFRACTIONn_angle_d

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