+Open data
-Basic information
Entry | Database: PDB / ID: 146d | |||||||||||||||||||||
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Title | SOLUTION STRUCTURE OF THE MITHRAMYCIN DIMER-DNA COMPLEX | |||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / MITHRAMYCIN DIMER | Function / homology | Chem-CRH / DNA | Function and homology information Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | Authors | Sastry, M. / Patel, D.J. | Citation | Journal: Biochemistry / Year: 1993 | Title: Solution structure of the mithramycin dimer-DNA complex. Authors: Sastry, M. / Patel, D.J. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 146d.cif.gz | 38.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb146d.ent.gz | 31.5 KB | Display | PDB format |
PDBx/mmJSON format | 146d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/46/146d ftp://data.pdbj.org/pub/pdb/validation_reports/46/146d | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | #4: Chemical | ChemComp-MG / | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR details | Text: THE HYDROXYL PROTONS IN THE RELAXATION MATRIX REFINED STRUCTURES ARE NOT WELL DETERMINED. THE HYDROPHILIC SIDE CHAIN, THE B SUGAR RESIDUE DDA 1 AND DDA 7, AND RESIDUES T 1 AND C 2 ARE UNDETERMINED. |
-Processing
Software |
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NMR software | Name: X-PLOR / Version: 2.1 / Developer: Brunger / Classification: refinement | ||||||||
Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE ...Details: TWO STARTING MODELS WERE OBTAINED BY DOCKING THE MG2+ COORDINATED MITHRAMYCIN DIMER IN THE MINOR GROOVE OF A AND B FORM D(TCGCGA) DUPLEX. THESE MODELS WERE SUBSEQUENTLY REFINED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. THE TWO DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL TWO STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND MINIMIZED. THE R VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE R FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE TWO FINAL STRUCTURES ARE: MODEL 1 MODEL 2 R FACTOR 0.146 0.136 BOND (ANGSTROMS) 0.016 0.013 ANGLES (DEGREES) 3.410 3.369. THE STRUCTURE EXHIBITS APPROXIMATE TWO-FOLD SYMMETRY, PERPENDICULAR TO THE HELICAL AXIS AND PASSING THROUGH THE MAGNESIUM IN THE COMPLEX. THE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 1 WHEN APPLIED TO CHAIN A OF MODEL 1. THE TRANSFORMATION PRESENTED ON *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN B OF MODEL 2 WHEN APPLIED TO CHAIN A OF MODEL 2. | ||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 2 / Conformers submitted total number: 2 |