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Yorodumi- PDB-5jvw: Crystal structure of mithramycin analogue MTM SA-Trp in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jvw | ||||||||||||||||||||
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Title | Crystal structure of mithramycin analogue MTM SA-Trp in complex with a 10-mer DNA AGAGGCCTCT. | ||||||||||||||||||||
Components | DNA (5'-D(*Keywords | dna/antibiotic / anti-cancer agent / Ewing sarcoma / transcription factor / minor groove / DNA binding / dna-antibiotic complex | Function / homology | Plicamycin, mithramycin analogue MTM SA-Trp / DNA | Function and homology information Biological species | synthetic construct (others) | Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | Authors | Hou, C. / Rohr, J. / Tsodikov, O.V. | Citation | Journal: Nucleic Acids Res. / Year: 2016 | Title: Structures of mithramycin analogues bound to DNA and implications for targeting transcription factor FLI1. Authors: Hou, C. / Weidenbach, S. / Cano, K.E. / Wang, Z. / Mitra, P. / Ivanov, D.N. / Rohr, J. / Tsodikov, O.V. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jvw.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jvw.ent.gz | 37.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/5jvw ftp://data.pdbj.org/pub/pdb/validation_reports/jv/5jvw | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | 1 complex of MTM SA-Trp with double-stranded DNA |
-Components
#1: DNA chain | Mass: 3045.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-6O6 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.83 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Incubation against 35% v/v 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 10439 / % possible obs: 95.8 % / Observed criterion σ(F): 1.74 / Redundancy: 3.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→40 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.135 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.282 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40 Å
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