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Yorodumi- PDB-1i5l: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i5l | ||||||
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Title | CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM1) FROM ARCHAEOGLOBUS FULGIDUS COMPLEXED WITH SHORT POLY-U RNA | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / SNRNP / SM / CORE SNRNP DOMAIN / RNA BINDING PROTEIN / SINGLE-STRANDED RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information Lsm1-7-Pat1 complex / intracellular organelle / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D. | ||||||
Citation | Journal: EMBO J. / Year: 2001 Title: RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex. Authors: Toro, I. / Thore, S. / Mayer, C. / Basquin, J. / Seraphin, B. / Suck, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i5l.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i5l.ent.gz | 154.2 KB | Display | PDB format |
PDBx/mmJSON format | 1i5l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i5/1i5l ftp://data.pdbj.org/pub/pdb/validation_reports/i5/1i5l | HTTPS FTP |
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-Related structure data
Related structure data | 1i4kSC 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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1 |
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2 |
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Unit cell |
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Details | : The 14 monomers are organized in two ring-shaped heptamers. |
-Components
#1: RNA chain | Mass: 873.540 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 8391.709 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF0875 / Plasmid: MODIFIED PET24D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O29386 #3: Chemical | ChemComp-URI / #4: 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: 2.42 Å3/Da / Density % sol: 49.11 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.4 Details: PEG6000, sodium citrate, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.3 | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 27, 2000 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→25 Å / Num. all: 28746 / Num. obs: 28746 / % possible obs: 97.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 82.323 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.75→2.9 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique all: 4203 / Rsym value: 0.354 / % possible all: 97.5 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 70211 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 97.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I4K Resolution: 2.75→25 Å / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 82.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.75→2.92 Å / Rfactor Rfree error: 0.029
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor obs: 0.225 / Rfactor Rfree: 0.3 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 82.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.458 / Rfactor Rwork: 0.392 |