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Yorodumi- PDB-1kxk: Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kxk | ||||||
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Title | Crystal Structure of a RNA Molecule Containing Domain 5 and 6 of the Yeast ai5g Group II Self-splicing Intron | ||||||
Components | ai5g group II Self-splicing intron | ||||||
Keywords | RNA / double helix / tetraloop / tetraloop receptor / two-nucleotide bulge | ||||||
Function / homology | RNA / RNA (> 10) Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å | ||||||
Authors | Zhang, L. / Doudna, J.A. | ||||||
Citation | Journal: Science / Year: 2002 Title: Structural insights into group II intron catalysis and branch-site selection. Authors: Zhang, L. / Doudna, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kxk.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kxk.ent.gz | 34.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kxk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kxk_validation.pdf.gz | 382.3 KB | Display | wwPDB validaton report |
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Full document | 1kxk_full_validation.pdf.gz | 386.8 KB | Display | |
Data in XML | 1kxk_validation.xml.gz | 4.4 KB | Display | |
Data in CIF | 1kxk_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kxk ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kxk | 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: RNA chain | Mass: 22620.477 Da / Num. of mol.: 1 / Fragment: domain 5 and 6 / Source method: obtained synthetically Details: THE SEQUENCE IS FROM Saccharomyces cerevisiae (yeast). in vitro transcription. |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 6.23 Å3/Da / Density % sol: 80.26 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: HEPES-KOH, magnesium chloride, ammonium sulfate, spermine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 25 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3→30 Å / Num. all: 12289 / Num. obs: 10014 / % possible obs: 81.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 15.5 % / Rsym value: 0.054 / Net I/σ(I): 23.4 | ||||||||||||||||||
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.43 / % possible all: 51.7 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 30 Å / % possible obs: 85.8 % / Rmerge(I) obs: 0.054 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 51.7 % / Rmerge(I) obs: 0.43 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3→30 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→30 Å
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LS refinement shell | Resolution: 3→3.11 Å
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Refinement | *PLUS Lowest resolution: 30 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.4186 |