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Yorodumi- PDB-1i81: CRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1i81 | ||||||
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Title | CRYSTAL STRUCTURE OF A HEPTAMERIC LSM PROTEIN FROM METHANOBACTERIUM THERMOAUTOTROPHICUM | ||||||
Components | PUTATIVE SNRNP SM-LIKE PROTEIN | ||||||
Keywords | STRUCTURAL GENOMICS / Curved anti-parallel beta sheet | ||||||
Function / homology | Function and homology information Sm-like protein family complex / intracellular organelle / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Collins, B.M. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M.G. / Mabbutt, B.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. Authors: Collins, B.M. / Harrop, S.J. / Kornfeld, G.D. / Dawes, I.W. / Curmi, P.M. / Mabbutt, B.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1i81.cif.gz | 111.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1i81.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 1i81.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/1i81 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/1i81 | HTTPS FTP |
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-Related structure data
Related structure data | 1b34S 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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Unit cell |
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-Components
#1: Protein | Mass: 9184.438 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: MT0649 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (AMERSHAM PHARMACIA BIOTECH) / References: UniProt: O26745 #2: 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: 2.13 Å3/Da / Density % sol: 42.35 % | ||||||||||||||||||||
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tris PEG3350 Lithium sulphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294.0K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 1, 2000 / Details: Focusing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2 Å / Num. all: 119267 / Num. obs: 119267 / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.7 |
Reflection | *PLUS Lowest resolution: 15 Å / Num. obs: 35595 / % possible obs: 98.2 % / Num. measured all: 119267 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 85.6 % / Rmerge(I) obs: 0.307 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Model constructed from 1B34 Resolution: 2→15 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.257 / Rfactor Rwork: 0.218 / % reflection Rfree: 7.5 % | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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