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Yorodumi- PDB-3uyb: X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uyb | |||||||||||||||||||||
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Title | X-ray crystal structure of the ruthenium complex [Ru(tap)2(dppz)]2+ bound to d(TCGGTACCGA) | |||||||||||||||||||||
Components | 5'-D(*Keywords | DNA / DNA-Ruthenium complex / Semiintercalation / intercalation / Minor groove interaction | Function / homology | : / Ru(tap)2(dppz) complex / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | Authors | Niyazi, H.N. / Texeira, S.C.M. / Mitchell, E.P. / Cardin, J.C. / Forsyth, V.T. | Citation | Journal: To be Published | Title: Crystal structure of lambda-[Ru(TAP)2(dppz)]2+ with d(TCGGTACCGA)2 displaying kinking of DNA via semiintercalation. Authors: Niyazi, H.N. / O'Sullivan, K. / Texeira, S.C.M. / Mitchell, E.P. / Kelly, J.M. / Cardin, J.C. / Forsyth, V.T. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uyb.cif.gz | 30.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uyb.ent.gz | 21.8 KB | Display | PDB format |
PDBx/mmJSON format | 3uyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/3uyb ftp://data.pdbj.org/pub/pdb/validation_reports/uy/3uyb | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar 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: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: Chemical | #3: Chemical | ChemComp-BA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGTACCGA), 1mM lambda-[Ru(tap)2dppz)Cl2 , pH 7.0, ...Details: 10%(v/v) 2-methyl-2,4-pentanediol, 40mM sodium cacodylate, 12mM spermine tetra-HCl, 80mM sodium chloride, 20mM barium chloride, 1mM DNA d(TCGGTACCGA), 1mM lambda-[Ru(tap)2dppz)Cl2 , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.984 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.45 Å / Num. obs: 7382 / % possible obs: 99.9 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 1.7 |
Reflection shell | Resolution: 1.5→1.58 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→38.45 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.074 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 1.7 / ESU R: 0.068 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 19.742 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→38.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -42.417 Å / Origin y: -39.996 Å / Origin z: 16.947 Å
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Refinement TLS group |
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