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- PDB-427d: 5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3' -

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Basic information

Entry
Database: PDB / ID: 427d
Title5'-D(*CP*GP*CP*(CH2-DM1)GP*CP*G)-3'
ComponentsDNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')
KeywordsDNA / DEOXYRIBONUCLEIC ACID / DRUG COMPLEX / FORMALDEHYDE CROSS-LINK / ATOMIC RESOLUTION / DOUBLE BACKBONE CONFORMATION
Function / homologyDAUNOMYCIN / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsSchuerman, G. / Van Meervelt, L.
CitationJournal: J.Am.Chem.Soc. / Year: 2000
Title: Conformational Flexibility of the DNA Backbone.
Authors: Schuerman, G. / Van Meervelt, L.
History
DepositionSep 21, 1998Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,3522
Polymers1,8241
Non-polymers5281
Water1,17165
1
A: DNA (5'-D(*CP*GP*CP*(G49)P*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)4,7044
Polymers3,6482
Non-polymers1,0552
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)27.818, 27.818, 51.858
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 DNA (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-DM1 / DAUNOMYCIN / DAUNORUBICIN


Mass: 527.520 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.31 % / Description: DDF023 USED AS STARTING MODEL FOR REFINEMENT
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2NACL11
3BACL211
4SPERMINE11
5MPD11
6MPD12
Crystal grow
*PLUS
Temperature: 16 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.0 mMoligonucleotide1drop
26.4 mMdaunomycin HCl1drop
310 %MPD1drop
412 mMspermine tetrachloride1drop
580 mM1dropNaCl
620 mM1dropBaCl2
835 %MPD1reservoir
7sodium cacodylate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.1→15 Å / Num. all: 8581 / Num. obs: 8581 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 25.27
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.094 / Mean I/σ(I) obs: 10.58 / % possible all: 77
Reflection
*PLUS
% possible obs: 97.3 %
Reflection shell
*PLUS
% possible obs: 77 % / Num. unique obs: 338

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Processing

Software
NameClassification
SHELXLrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: DDF023

Resolution: 1.1→15 Å / Num. parameters: 2327 / σ(F): 4 / Details: ANISOTROPIC UNRESTRAINED REFIN.
RfactorNum. reflection% reflection
all0.1021 8581 -
obs0.1007 -97.5 %
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201- 228
Refine analyzeNum. disordered residues: 27 / Occupancy sum hydrogen: 222.47 / Occupancy sum non hydrogen: 97
Refinement stepCycle: LAST / Resolution: 1.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 182 0 75 257
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 8277 / Rfactor all: 0.102 / Rfactor obs: 0.101
Solvent computation
*PLUS
Displacement parameters
*PLUS

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