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- PDB-366d: 1.3 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/6-BROMO-9-A... -

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Basic information

Entry
Database: PDB / ID: 366d
Title1.3 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/6-BROMO-9-AMINO-DACA COMPLEX
ComponentsDNA (5'-D(*CP*GP*(BRU)P*AP*CP*G)-3')
KeywordsDNA / DRUG INTERCALATION / MAJOR GROOVE BINDING
Function / homologyChem-DA6 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.3 Å
AuthorsTodd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Cardin, C.J.
CitationJournal: J.Med.Chem. / Year: 1999
Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethylamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray ...Title: Major groove binding and 'DNA-induced' fit in the intercalation of a derivative of the mixed topoisomerase I/II poison N-(2-(dimethylamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5-BrU)ACG)2 at 1.3-A resolution.
Authors: Todd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Wakelin, L.P. / Cardin, C.J.
History
DepositionDec 19, 1997Deposition site: NDB / Processing site: NDB
Revision 1.0Apr 6, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,6533
Polymers1,8741
Non-polymers7792
Water54030
1
A: DNA (5'-D(*CP*GP*(BRU)P*AP*CP*G)-3')
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)5,3056
Polymers3,7482
Non-polymers1,5574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)30.110, 30.110, 39.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Cell settinghexagonal
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-3015-

DA6

21A-3015-

DA6

31A-3015-

DA6

41A-3015-

DA6

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Components

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


Mass: 1874.087 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: COMPLEXED WITH 6-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE
#2: Chemical ChemComp-DA6 / 6-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE / 6BR20686


Mass: 389.290 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21BrN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.74 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1SODIUM CACODYLATE11
2MGCL211
3SPERMINE11
4MPD11
Crystal grow
*PLUS
Temperature: 285 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.5 mMDNA1drop
250 mMcacodylate1drop
32.0 mMmagnesium acetate1drop
43.0 mMsperine-4HCl1drop
55 %MPD1drop
630 %MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 14, 1997 / Details: MIRRORS
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→8 Å / Num. obs: 9362 / % possible obs: 95.3 % / Redundancy: 3.91 % / Rmerge(I) obs: 0.06
Reflection
*PLUS
Num. obs: 9306 / Num. measured all: 31514 / Rmerge(I) obs: 0.0675
Reflection shell
*PLUS
Highest resolution: 1.3 Å / Lowest resolution: 1.4 Å / % possible obs: 37 %

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-96refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.3→8 Å / Num. parameters: 3275 / Num. restraintsaints: 8013
RfactorNum. reflection% reflection
all0.185 8867 -
obs--90.2 %
Refine analyzeNum. disordered residues: 1 / Occupancy sum non hydrogen: 401.5
Refinement stepCycle: LAST / Resolution: 1.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 215 91 30 336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.002
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1468
Solvent computation
*PLUS
Displacement parameters
*PLUS

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