+Open data
-Basic information
Entry | Database: PDB / ID: 1ekh | ||||||||||||||||||||||||
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Title | NMR STRUCTURE OF D(TTGGCCAA)2 BOUND TO CHROMOMYCIN-A3 AND COBALT | ||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / drug bound in the minor groove of DNA | Function / homology | : / Chem-CPH / DNA | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Gochin, M. | Citation | Journal: Structure Fold.Des. / Year: 2000 Title: A high-resolution structure of a DNA-chromomycin-Co(II) complex determined from pseudocontact shifts in nuclear magnetic resonance. Authors: Gochin, M. #1: Journal: J.Am.Chem.Soc. / Year: 1999 Title: Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints Authors: Tu, K. / Gochin, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ekh.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ekh.ent.gz | 94.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ekh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ekh_validation.pdf.gz | 670.9 KB | Display | wwPDB validaton report |
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Full document | 1ekh_full_validation.pdf.gz | 786.5 KB | Display | |
Data in XML | 1ekh_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 1ekh_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekh ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekh | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: TWO MOLECULES OF THE DRUG CHROMOMYCIN A3 (1GL-2GL-DXB-DDA-DDA-1AR, CHAINS C, AND D) ARE BOUND IN THE MINOR GROOVE #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-CO / | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING PSEUDOCONTACT SHIFTS IN THE NMR SPECTRUM. PSEUDOCONTACT SHIFTS WERE MEASURED AS THE DIFFERENCE IN THE CHEMICAL SHIFT BETWEEN THE CO(II) COMPLEX AND THE ZN(II) ...Text: THE STRUCTURE WAS DETERMINED USING PSEUDOCONTACT SHIFTS IN THE NMR SPECTRUM. PSEUDOCONTACT SHIFTS WERE MEASURED AS THE DIFFERENCE IN THE CHEMICAL SHIFT BETWEEN THE CO(II) COMPLEX AND THE ZN(II) COMPLEX. IN MODELS 1-3, ONLY SHIFTS WERE USED; IN MODELS 4-6 SHIFTS + NOE'S WERE USED IN REFINEMENT. |
-Sample preparation
Details | Contents: D2O, 90% H2O, 10% D2O |
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Sample conditions | Ionic strength: 100mM NACL / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: GE OMEGA500 / Manufacturer: GE / Model: OMEGA500 / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Paramagnetic Shifts and NOEs used in refinement. Other REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: MINIMIZED AVERAGED COORDINATES FROM 6 RUNS Conformers calculated total number: 100 / Conformers submitted total number: 6 |