+Open data
-Basic information
Entry | Database: PDB / ID: 3i5l | ||||||||||||||||||
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Title | Allosteric Modulation of DNA by Small Molecules | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Cyclic Polyamide / DNA Binder / Minor Groove Binder / PyIm Polyamide | Function / homology | Chem-1P1 / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.18 Å | Authors | Chenoweth, D.M. / Dervan, P.B. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 | Title: Allosteric modulation of DNA by small molecules Authors: Chenoweth, D.M. / Dervan, P.B. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i5l.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i5l.ent.gz | 39.1 KB | Display | PDB format |
PDBx/mmJSON format | 3i5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i5l_validation.pdf.gz | 778.6 KB | Display | wwPDB validaton report |
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Full document | 3i5l_full_validation.pdf.gz | 784.6 KB | Display | |
Data in XML | 3i5l_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 3i5l_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/3i5l ftp://data.pdbj.org/pub/pdb/validation_reports/i5/3i5l | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3171.889 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid Phase Synthesis #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-1P1 / ( | #4: 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: 2.32 Å3/Da / Density % sol: 47.01 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 21% 2-methyl-2,4-pentanediol (MPD), 35 mM calcium acetate, 10 mM Tris pH 7.5 equilibrated in sitting drops against a reservoir of 35% MPD at 4 C. , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.175→26.472 Å / Num. obs: 19011 / Redundancy: 4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.175→1.205 Å / Redundancy: 4 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.9 / % possible all: 90.16 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.18→26.47 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.816 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 5.679 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→26.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.175→1.205 Å / Total num. of bins used: 20
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