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Yorodumi- PDB-2gwq: Crystal structure of D(G4T4G4) with four quadruplexes in the asym... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gwq | ||||||||||||||||||
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Title | Crystal structure of D(G4T4G4) with four quadruplexes in the asymmetric unit. | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / OXYTRICHA / G-QUARTET / G-QUADRUPLEX / G-TETRAD / G-TETRAPLEX / FOUR QUADRUPLEXES / ASYMMETRIC UNIT. | Function / homology | : / DNA / DNA (> 10) | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | Authors | Lee, M.P.H. / Parkinson, G.N. / Neidle, S. | Citation | Journal: To be Published | Title: Crystal structure of D(G4T4G4) with four and six quadruplexes in the asymmetric unit. Authors: Lee, M.P.H. / Haider, S. / Parkinson, G.N. / Neidle, S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gwq.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gwq.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 2gwq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gwq_validation.pdf.gz | 411.7 KB | Display | wwPDB validaton report |
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Full document | 2gwq_full_validation.pdf.gz | 413.9 KB | Display | |
Data in XML | 2gwq_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 2gwq_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/2gwq ftp://data.pdbj.org/pub/pdb/validation_reports/gw/2gwq | HTTPS FTP |
-Related structure data
Related structure data | 2gweC 1jrnS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3805.460 Da / Num. of mol.: 8 / Source method: obtained synthetically / Details: OXYTRICHA NOVA TELOMERIC SEQUENCE #2: Chemical | ChemComp-K / #3: 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: 2.21 Å3/Da / Density % sol: 44.3 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / pH: 6.5 Details: MAGNESIUM CHLORIDE, DNA, POTASSIUM CHLORIDE, MPD, PEPTIDE CONJUGATE BIS RKKV ACRIDONE, SPERMINE TETRAHYDROCHLORIDE, POTASSIUM CACODYLATE BUFFER, VAPOR DIFFUSION, HANGING DROP, temperature 285K, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.862451 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2003 / Details: A CYLINDRICAL GRAZING INCIDENCE MIRROR |
Radiation | Monochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.862451 Å / Relative weight: 1 |
Reflection | Resolution: 2→17 Å / Num. obs: 18992 / % possible obs: 96.6 % / Observed criterion σ(I): -2 / Redundancy: 3.35 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 26.27 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 8.74 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA PART OF NDB ENTRY CODE UD0014 OR PDB ENTRY CODE 1JRN. Resolution: 2→8 Å / Num. parameters: 8867 / Num. restraintsaints: 10018 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.84 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2213 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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