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Yorodumi- PDB-6kfl: Crystal structure of a two-quartet DNA G-quadruplex complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kfl | ||||||||||||||||||||||||||||
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Title | Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4 | ||||||||||||||||||||||||||||
Components | DNA (5'-D(*Keywords | DNA / G-quadruplex / two-quartet / complex | Function / homology | : / COBALT HEXAMMINE(III) / Chem-POH / DNA / DNA (> 10) | Function and homology information Biological species | Pseudorabies virus Ea | Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | Authors | Zhang, Y.S. / Parkinson, G.N. / Wei, D.G. | Funding support | China, 1items |
Citation | Journal: To Be Published | Title: Crystal structure of a two-quartet DNA G-quadruplex complexed with the porphyrin TMPyP4 Authors: Zhang, Y.S. / Parkinson, G.N. / Wei, D.G. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kfl.cif.gz | 52.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kfl.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 6kfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kfl_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6kfl_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6kfl_validation.xml.gz | 4 KB | Display | |
Data in CIF | 6kfl_validation.cif.gz | 5.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/6kfl ftp://data.pdbj.org/pub/pdb/validation_reports/kf/6kfl | HTTPS FTP |
-Related structure data
Related structure data | 6jjfS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 4362.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudorabies virus Ea / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-POH / ( | #4: Chemical | ChemComp-NCO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.28 Å3/Da / Density % sol: 46.12 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: KCaco,Nacaco,KCl,NaCl,hexammine cobalt(III) chloride,MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03923 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03923 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 5961 / % possible obs: 96.22 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.81 |
Reflection shell | Resolution: 1.92→1.989 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.354 / Num. unique obs: 487 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JJF Resolution: 1.92→35.063 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 31.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.96 Å2 / Biso mean: 34.7276 Å2 / Biso min: 7.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.92→35.063 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
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Refinement TLS params. | Method: refined / Origin x: 12.5944 Å / Origin y: -7.8122 Å / Origin z: 9.663 Å
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Refinement TLS group |
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