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- PDB-1mp7: A Third Complex of Post-Activated Neocarzinostatin Chromophore wi... -

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Basic information

Entry
Database: PDB / ID: 1mp7
TitleA Third Complex of Post-Activated Neocarzinostatin Chromophore with DNA. Bulge DNA Binding from the Minor Groove
Components5'-D(*GP*CP*CP*AP*GP*AP*GP*AP*GP*C)-3'
KeywordsDNA / DNA-drug complex / bulge DNA / recognition of anticancer
Function / homologyChem-NCG / DNA
Function and homology information
MethodSOLUTION NMR / distance geometry, simulated annealing, restrained molecular dynamics
AuthorsKwon, Y. / Xi, Z. / Kappen, L.S. / Goldberg, I.H. / Gao, X.
CitationJournal: Biochemistry / Year: 2003
Title: New Complex of Post-Activated Neocarzinostatin Chromophore with DNA: Bulge DNA Binding from the Minor Groove
Authors: Kwon, Y. / Xi, Z. / Kappen, L.S. / Goldberg, I.H. / Gao, X.
History
DepositionSep 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-D(*GP*CP*CP*AP*GP*AP*GP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0482
Polymers3,0791
Non-polymers9691
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)9 / 9all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

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


Mass: 3079.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Chemical ChemComp-NCG / [(R)-4-((1,3-DIOXOLANE-2-OXY)-4-(S)-YL)-4-HYDROXY]-(R)-10-(2-METHYLAMINO-5-METHYL-2,6-DIDEOXYGALACTOPYRANOSYL-OXY)-(R)-11-(2-HYDROXY-5-METHYL-7-METHOXY-1-NAPHTHOYL-OXY)-(R)-12-S-GLUTATHIONYL-4,10,11,12-TETRAHYDROINDACENE / NCSI-GLU / NEOCARZINOSTATIN-GLUTATHIONE CHROMOPHORE


Mass: 968.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H52N4O18S

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
2222D TOCSY
232DQF-COSY
242H-P COSY, COSY-45, T1 measurement, Translational diffusion constant measurement
NMR detailsText: This structure was determined using standard 2D homonuclear and heteronuclear (1H-31P) techniques. Diffusion constant measurement experiment was used to address the conformation of the complex ...Text: This structure was determined using standard 2D homonuclear and heteronuclear (1H-31P) techniques. Diffusion constant measurement experiment was used to address the conformation of the complex adopting either homoduplex or self-folded hairpin form.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mM DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.090% H2O-10% D2O, 100% D2O
20.9mM complex of NCSi-glu-bulge DNA; 10 mM phophate buffer containing 0.1 mM EDTA, pH 6.090% H2O-10% D2O, 100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 6.0 ambient 273 K
210 mM Sodium Phosphate, 0.1 mM EDTA, pH 6.0 6.0 ambient 268 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker AMXBrukerAMX6002

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Processing

NMR software
NameVersionDeveloperClassification
UXNMRAspect X32Brukercollection
Felix98 and 2000Accelrysprocessing
X-PLOR3.851Axel T. Brungerstructure solution
MARDIGRAS3Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumardata analysis
X-PLOR3.851Axel T. Brungerrefinement
RefinementMethod: distance geometry, simulated annealing, restrained molecular dynamics
Software ordinal: 1
Details: the structure calculation was based on a total of 316 restraints, 258 NOE-derived distance constraints, 40 of dihedral angle restraints, and 18 distance restraints from hydrogen bonds of Wason-Creek base pairs.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable ...Conformer selection criteria: all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 9 / Conformers submitted total number: 9

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