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Yorodumi- PDB-3ktw: Crystal structure of the SRP19/S-domain SRP RNA complex of Sulfol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ktw | ||||||
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Title | Crystal structure of the SRP19/S-domain SRP RNA complex of Sulfolobus solfataricus | ||||||
Components |
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Keywords | RNA/RNA binding protein / ribonucleoprotein complex / RNA-RNA tertiary interactions / asymmetric loop / 7S RNA / signal recognition particle / structural RNA / RNA-binding / RNA-RNA binding protein complex | ||||||
Function / homology | Function and homology information signal recognition particle / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Wild, K. / Bange, G. / Bozkurt, G. / Sinning, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: Structural insights into the assembly of the human and archaeal signal recognition particles. Authors: Wild, K. / Bange, G. / Bozkurt, G. / Segnitz, B. / Hendricks, A. / Sinning, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ktw.cif.gz | 161.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ktw.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 3ktw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ktw_validation.pdf.gz | 480 KB | Display | wwPDB validaton report |
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Full document | 3ktw_full_validation.pdf.gz | 574 KB | Display | |
Data in XML | 3ktw_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 3ktw_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3ktw ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3ktw | HTTPS FTP |
-Related structure data
Related structure data | 3ktvC 1lngS C: citing same article (ref.) 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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2 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 31165.553 Da / Num. of mol.: 2 / Fragment: S domain Source method: isolated from a genetically manipulated source Details: in vitro transcription / Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Plasmid: pUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: GenBank: X17239.1 #2: Protein | Mass: 12939.142 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: srp19, SSO0165 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q980W2 #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-MG / |
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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: 3.58 Å3/Da / Density % sol: 65.62 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 100 mM Na cacodylate, 400 mM KCl, 10 mM CaCl2, 15% (w/v) PEG4000, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
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: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2006 / Details: mirrors |
Radiation | Monochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→64.7 Å / Num. all: 20744 / Num. obs: 20578 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rsym value: 0.092 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.388 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1LNG Resolution: 3.2→64.68 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.527 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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 max: 184.16 Å2 / Biso mean: 86.721 Å2 / Biso min: 32.73 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→64.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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