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- PDB-2k4l: Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benz... -

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Basic information

Entry
Database: PDB / ID: 2k4l
TitleSolution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benzodiazepine (PBD) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.
Components5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3'
KeywordsDNA / pyrrolo[2 / 1-c][1 / 4]benzodiazepine / PBD / DNA Adduct
Function / homologyChem-PZD / DNA / DNA (> 10)
Function and homology information
MethodSOLUTION NMR / simulated annealing
AuthorsAntonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M.
Citation
Journal: Biochemistry / Year: 2008
Title: Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization.
Authors: Antonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M.
#1: Journal: J.Comb.Chem. / Year: 2007
Title: Parallel Synthesis of a Novel C2-Aryl Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) Library
Authors: Antonow, D. / Cooper, N. / Howard, P.W. / Thurston, D.E.
History
DepositionJun 13, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3'
B: 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3294
Polymers8,5562
Non-polymers7732
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: DNA chain 5'-D(*DAP*DAP*DTP*DCP*DTP*DTP*DTP*DAP*DAP*DAP*DGP*DAP*DTP*DT)-3'


Mass: 4277.827 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE ...Details: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE DUPLEX WAS FORMED BY ANNEALING IN PHOSPHATE BUFFER.
#2: Chemical ChemComp-PZD / (11aS)-7,8-dimethoxy-2-naphthalen-2-yl-1,10,11,11a-tetrahydro-5H-pyrrolo[2,1-c][1,4]benzodiazepin-5-one


Mass: 386.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H22N2O3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H COSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.68 mM / Component: DNA
Sample conditionsIonic strength: 130 / pH: 6.85 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.16Schwieters, Kuszewski, Tjandra and Clorerefinement
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
AMIX3.5.5Bruker Biospinpeak picking
AMIX3.5.5Bruker Biospinchemical shift assignment
RefinementMethod: simulated annealing / Software ordinal: 1
Details: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE ...Details: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE ROOT MEAN SQUARE DEVIATION VALUES CALCULATED.
NMR constraintsNOE constraints total: 374 / NOE intraresidue total count: 174 / NOE long range total count: 40 / NOE medium range total count: 18 / NOE sequential total count: 102
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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