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- PDB-107d: SOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX -

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Entry
Database: PDB / ID: 107d
TitleSOLUTION STRUCTURE OF THE COVALENT DUOCARMYCIN A-DNA DUPLEX COMPLEX
Components
  • DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3')
  • DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')
KeywordsDNA / DOUBLE HELIX
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsLin, C.H. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution structure of the covalent duocarmycin A-DNA duplex complex.
Authors: Lin, C.H. / Patel, D.J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 17, 1995 / Release: May 8, 1995
RevisionDateData content typeGroupProviderType
1.0May 8, 1995Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)4,7443
Polyers4,2352
Non-polymers5101
Water0
NMR ensembles
Datacriteria
Number of conformers (submitted / calculated)4 / -
Representative

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Components

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


Mass: 2039.359 Da / Num. of mol.: 1 / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')


Mass: 2195.487 Da / Num. of mol.: 1 / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Chemical ChemComp-DUO / 4-HYDROXY-2,8-DIMETHYL-1-OXO-6-(4,5,6-TRIMETHOXY-1H-INDOLE-2-CARBONYL)-1,2,3,6,7,8-HEXAHYDRO-3,6-DIAZA-AS-INDACENE-2-CARBOXYLIC ACID METHYL ESTER / DUOCARMYCIN A


Mass: 509.508 Da / Num. of mol.: 1 / Formula: C26H27N3O8 / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: DUOCARMYCIN A WAS PROVIDED BY KYOWA HAKKO KOGYO CO., JAPAN.

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
RefinementMethod: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1
Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA. ONE INITIAL VELOCITY SEED WAS USED FOR EACH STARTING STRUCTURE WHICH YIELDS TWO DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER WITH TWO INITIAL VELOCITIES USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS TO GENERATE THE FINAL FOUR STRUCTURES. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 40, 80, 120 AND 160 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1-MODEL4 R(1/6) FACTOR 0.042-0.045 BOND (ANG) 0.009-0.010 ANGLES (DEG) 3.078-3.780 IMPROPERS (DEG) 0.310-0.321. THE STRUCTURE HAS APPROXIMATE TWO-FOLD SYMMETRY RELATING THE TWO STRANDS OF THE DNA WITH THE SYMMETRY AXIS PERPENDICULAR TO THE HELICAL AXIS. THE TRANSFORMATION MATRIX WAS CALCULATED FOR THE AVERAGED STRUCTURE OF THE FOUR MODELS.
NMR ensembleConformers submitted total number: 4

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