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Yorodumi- PDB-1kgk: Direct Observation of a Cytosine Analog that Forms Five Hydrogen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kgk | ||||||||||||||||||
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Title | Direct Observation of a Cytosine Analog that Forms Five Hydrogen Bonds to Guanosine; Guanyl G-Clamp | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / A-form Double Helix / cytosine analogue | Function / homology | METHOXY-ETHOXYL / SPERMINE (FULLY PROTONATED FORM) / DNA | Function and homology information Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å | Authors | Wilds, C.J. / Maier, M.A. / Tereshko, V. / Manoharan, M. / Egli, M. | Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2002 | Title: Direct Observation of a Cytosine Analogue that Forms Five Hydrogen Bonds to Guanosine: Guanidino G-Clamp Authors: Wilds, C.J. / Maier, M.A. / Tereshko, V. / Manoharan, M. / Egli, M. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kgk.cif.gz | 48.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kgk.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 1kgk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kgk_validation.pdf.gz | 409.6 KB | Display | wwPDB validaton report |
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Full document | 1kgk_full_validation.pdf.gz | 416.2 KB | Display | |
Data in XML | 1kgk_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1kgk_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/1kgk ftp://data.pdbj.org/pub/pdb/validation_reports/kg/1kgk | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3237.199 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Solid phase chemical synthesis. #2: Chemical | #3: Chemical | ChemComp-SPK / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.07 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: hanging drop / pH: 6 Details: 1.2 mM DNA, 5% MPD, 20 mM Sodium Cacodylate, 40 mM sodium chloride, 6 mM potassium chloride, 10 mM magnesium chloride; equilibrated against 35% MPD, pH 6.0, Hanging Drop, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.978 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 29, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1→10 Å / Num. all: 27320 / Num. obs: 27320 / % possible obs: 99.6 % / Rmerge(I) obs: 0.047 |
Reflection shell | Resolution: 1→1.1 Å / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 20 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→10 Å / Num. parameters: 5528 / Num. restraintsaints: 26595
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Refine analyze | Occupancy sum hydrogen: 283.5 / Occupancy sum non hydrogen: 608 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Highest resolution: 1 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 % | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1 Å / Lowest resolution: 1.1 Å / Num. reflection obs: 6666 / Rfactor all: 0.13 |