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- PDB-274d: CRYSTAL STRUCTURE OF A COVALENT DNA-DRUG ADDUCT: ANTHRAMYCIN BOUN... -

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Entry
Database: PDB / ID: 274d
TitleCRYSTAL STRUCTURE OF A COVALENT DNA-DRUG ADDUCT: ANTHRAMYCIN BOUND TO C-C-A-A-C-G-T-T-G-G, AND A MOLECULAR EXPLANATION OF SPECIFICITY
ComponentsDNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*(DRUG)GP*G)-3')
KeywordsDNA / B-DNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyANTHRAMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsKopka, M.L. / Goodsell, D.S. / Baikalov, I. / Grzeskowiak, K. / Cascio, D. / Dickerson, R.E.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of a covalent DNA-drug adduct: anthramycin bound to C-C-A-A-C-G-T-T-G-G and a molecular explanation of specificity.
Authors: Kopka, M.L. / Goodsell, D.S. / Baikalov, I. / Grzeskowiak, K. / Cascio, D. / Dickerson, R.E.
History
DepositionApr 28, 1994Deposition site: BNL / Processing site: NDB
Revision 1.0Oct 21, 1994Provider: 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_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*(DRUG)GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,3602
Polymers3,0451
Non-polymers3151
Water39622
1
A: DNA (5'-D(*CP*CP*AP*AP*CP*GP*TP*TP*(DRUG)GP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,7214
Polymers6,0902
Non-polymers6312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Unit cell
Length a, b, c (Å)23.950, 23.950, 88.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-ANT / ANTHRAMYCIN


Mass: 315.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H17N3O4 / Comment: antitumor, antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.42 Å3/Da / Density % sol: 49.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 277.00K
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2METHANOL11
3MPD11
4MGCL211
5WATER12
6MPD12

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Data collection

DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Num. obs: 1212 / Observed criterion σ(F): 2
Reflection
*PLUS
% possible obs: 90 % / Rmerge(I) obs: 0.0638

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Processing

SoftwareName: NUCLSQ / Classification: refinement
RefinementResolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection% reflection
obs0.212 1212 90 %
Refine Biso
ClassRefine-ID
ALL ATOMSX-RAY DIFFRACTION
ALL WATERSX-RAY DIFFRACTION
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 22 22 246
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONn_bond_d
X-RAY DIFFRACTIONn_angle_d
X-RAY DIFFRACTIONn_planar_d
X-RAY DIFFRACTIONn_hb_or_metal_coord
X-RAY DIFFRACTIONn_sugar_bond_it5.1026
X-RAY DIFFRACTIONn_sugar_angle_it6.5346
X-RAY DIFFRACTIONn_phos_bond_it6.2136
X-RAY DIFFRACTIONn_phos_angle_it6.7436
X-RAY DIFFRACTIONn_bond_angle_restr
X-RAY DIFFRACTIONn_dihedral_angle_restr
X-RAY DIFFRACTIONn_impr_tor
X-RAY DIFFRACTIONn_sugar_bond_d0.030.03
X-RAY DIFFRACTIONn_sugar_bond_angle_d0.0580.04
X-RAY DIFFRACTIONn_phos_bond_d0.0320.03
X-RAY DIFFRACTIONn_phos_bond_angle_d0.0610.04
X-RAY DIFFRACTIONn_plane_restr0.0180.02
X-RAY DIFFRACTIONn_chiral_restr0.2070.15
X-RAY DIFFRACTIONn_singtor_nbd0.0880.1
X-RAY DIFFRACTIONn_multtor_nbd0.1150.1
X-RAY DIFFRACTIONn_xhyhbond_nbd0.1830.1
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 8 Å / Num. reflection obs: 1212 / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34.26 Å2

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