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- PDB-367d: 1.2 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/5-BROMO-9-A... -

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Basic information

Entry
Database: PDB / ID: 367d
Title1.2 A STRUCTURE DETERMINATION OF THE D(CG(5-BRU)ACG)2/5-BROMO-9-AMINO-DACA COMPLEX
Components5'-D(*CP*GP*(BRU)P*AP*CP*G)-3'
KeywordsDNA / DOUBLE HELIX / COMPLEXED WITH DRUG / MODIFIED
Function / homologyBROMIDE ION / Chem-DA5 / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 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-(dimethlyamino)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-(dimethlyamino)ethyl)acridine-4-carboxamide (DACA) into DNA: X-ray structure complexed to d(CG(5Br-U)ACG)2 at 1.3-angstrom resolution
Authors: Todd, A.K. / Adams, A. / Thorpe, J.H. / Denny, W.A. / Wakelin, L.P.G. / Cardin, C.J.
History
DepositionDec 19, 1997Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: 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_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: 5'-D(*CP*GP*(BRU)P*AP*CP*G)-3'
B: 5'-D(*CP*GP*(BRU)P*AP*CP*G)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9187
Polymers3,5902
Non-polymers1,3285
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.096, 30.096, 39.547
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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


Mass: 1795.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#2: Chemical ChemComp-DA5 / 5-BROMO-9-AMINO-N-ETHYL(DIAMINOMETHYL)ACRIDINE-4-CARBOXAMIDE / 5BR20686


Mass: 389.290 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21BrN4O
#3: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.73 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5 / Details: pH 6.50
Components of the solutions
IDConc.NameCrystal-IDDetailsSol-IDVolume (Å3)
12 WATER1311
25 CACODYLATECacodylic acid1614
38 MG2+Magnesium1917
411 SPERMINE112110
514 MPD115113

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 1997 / Details: MIRRORS
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.2→12 Å / Num. obs: 11570 / % possible obs: 92.3 % / Redundancy: 3.242 % / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXLrefinement
RefinementResolution: 1.2→100 Å / Num. parameters: 3299 / Num. restraintsaints: 7900 / Cross valid method: NONE
RfactorNum. reflection% reflection
all0.178 10983 -
obs0.178 10983 87.7 %
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 415 / Occupancy sum non hydrogen: 0
Refinement stepCycle: LAST / Resolution: 1.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 238 80 113 431
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d
X-RAY DIFFRACTIONs_angle_d0.005
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

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