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- PDB-199d: Solution structure of the monoalkylated mitomycin c-DNA complex -

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Entry
Database: PDB / ID: 199d
TitleSolution structure of the monoalkylated mitomycin c-DNA complex
Components
  • DNA (5'-D(*(DI)P*CP*AP*CP*GP*TP*CP*(DI)P*T)-3')
  • DNA (5'-D(*AP*CP*GP*AP*CP*GP*TP*GP*C)-3')
KeywordsDNA / MITOMYCIN / DOUBLE HELIX
Function / homologyChem-MOC / DNA
Function and homology information
MethodSOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION
AuthorsSastry, M. / Fiala, R. / Lipman, R. / Tomasz, M. / Patel, D.J.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Solution structure of the monoalkylated mitomycin C-DNA complex.
Authors: Sastry, M. / Fiala, R. / Lipman, R. / Tomasz, M. / Patel, D.J.
History
DepositionDec 1, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / pdbx_entity_src_syn
Item: _entity.details

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: DNA (5'-D(*(DI)P*CP*AP*CP*GP*TP*CP*(DI)P*T)-3')
B: DNA (5'-D(*AP*CP*GP*AP*CP*GP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,7473
Polymers5,4432
Non-polymers3041
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 3all calculated structures submitted
Representative

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Components

#1: DNA chain DNA (5'-D(*(DI)P*CP*AP*CP*GP*TP*CP*(DI)P*T)-3')


Mass: 2701.770 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#2: DNA chain DNA (5'-D(*AP*CP*GP*AP*CP*GP*TP*GP*C)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / Keywords: DEOXYRIBONUCLEIC ACID
#3: Chemical ChemComp-MOC / CARBAMIC ACID 2,6-DIAMINO-5-METHYL-4,7-DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL ESTER


Mass: 304.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4O4 / Details: CHEMICALLY SYNTHESIZED

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: NMR

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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: THREE STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITOMYCIN C ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF ...Details: THREE STARTING STRUCTURES WERE OBTAINED BY MANUALLY DOCKING MITOMYCIN C ON A FORM AND B FORM DNA. THESE WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCES DERIVED FROM NMR DATA. THE THREE DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL THREE STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 90, 120, 200 AND 300 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE THREE FINAL STRUCTURES ARE: MDL1 MDL2 MDL3 R(1/6) FACTOR 0.027 0.026 0.026 BOND (ANG) 0.008 0.008 0.008 ANGLE (DEG) 2.913 2.931 2.949 IMPROPER (DEG) 0.361 0.393 0.372
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 3 / Conformers submitted total number: 3

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