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Yorodumi- PDB-1jri: The Crystal Structure of an Sm-like Archaeal Protein with Two Hep... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jri | ||||||
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Title | The Crystal Structure of an Sm-like Archaeal Protein with Two Heptamers in the Asymmetric Unit. | ||||||
Components | Sm-like Archaeal Protein 1 (SmAP1) | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / heptameric / 35-stranded beta toroid | ||||||
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: 2.8 Å | ||||||
Authors | Mura, C. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: The oligomerization and ligand-binding properties of Sm-like archaeal proteins (SmAPs) Authors: Mura, C. / Kozhukhovsky, A. / Gingery, M. / Phillips, M. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jri.cif.gz | 208.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jri.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jr/1jri ftp://data.pdbj.org/pub/pdb/validation_reports/jr/1jri | HTTPS FTP |
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-Related structure data
Related structure data | 1jbmSC 1lnxC 1lojC 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 asymmetric unit of the P212121 lattice contains two copies of the biologically significant assembly (a heptamer), the tangential rings being roughly coplanar (~15 degrees deviation). |
-Components
#1: Protein | Mass: 9502.921 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Gene: Mth0649 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745 #2: Chemical | #3: Chemical | ChemComp-EDO / #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: 2.08 Å3/Da / Density % sol: 40.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292.8 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, 10% v/v isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 19.8K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.8 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2001 / Details: fine-focussing mirrors |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 28487 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2.8→2.9 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2645 / % possible all: 92.5 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. measured all: 329838 |
Reflection shell | *PLUS % possible obs: 92.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JBM Resolution: 2.8→14.95 Å Isotropic thermal model: restrained isotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 52.3 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→14.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.97 Å / Rfactor Rfree error: 0.026
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.29 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 52.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Rfactor Rfree: 0.375 / Rfactor Rwork: 0.28 |