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Yorodumi- PDB-1loj: Crystal structure of a Methanobacterial Sm-like archaeal protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1loj | ||||||
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Title | Crystal structure of a Methanobacterial Sm-like archaeal protein (SmAP1) bound to uridine-5'-monophosphate (UMP) | ||||||
Components | small nuclear ribonucleoprotein homolog (Sm-like) | ||||||
Keywords | RNA BINDING PROTEIN / transcription / beta barrel / OB-fold / heptameric toroid / tetradecamer | ||||||
Function / homology | Function and homology information pICln-Sm protein complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Methanothermobacter thermautotrophicus str. Delta H (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mura, C. / Kozhukhovsky, A. / 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. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: The crystal structure of a heptameric archaeal Sm protein: Implications for the eukaryotic snRNP core Authors: Mura, C. / Cascio, D. / Sawaya, M.R. / Eisenberg, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1loj.cif.gz | 233.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1loj.ent.gz | 189.1 KB | Display | PDB format |
PDBx/mmJSON format | 1loj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1loj_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1loj_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1loj_validation.xml.gz | 50.5 KB | Display | |
Data in CIF | 1loj_validation.cif.gz | 69 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/1loj ftp://data.pdbj.org/pub/pdb/validation_reports/lo/1loj | HTTPS FTP |
-Related structure data
Related structure data | 1jbmSC 1jriC 1lnxC 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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2 |
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3 |
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Unit cell |
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Details | The asymmetric unit contains a tetradecamer of SmAP1 monomers arranged with pseudo-72 point group symmetry. The biological assembly is thought to be the heptamer formed by chains A through G (or H through N). Any biological significance of the 14-mer in the asymmetric unit is unknown. |
-Components
#1: Protein | Mass: 9645.075 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Details: full-length SmAP1 with additional 5-6 residues appended to the C-terminus (artefact of cloning vector) Source: (gene. exp.) Methanothermobacter thermautotrophicus str. Delta H (archaea) Species: Methanothermobacter thermautotrophicus / Strain: delta H / Gene: Mth649 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26745 #2: Chemical | ChemComp-U / #3: Chemical | ChemComp-MPD / ( #4: Chemical | ChemComp-URI / #5: 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: 2.38 Å3/Da / Density % sol: 47.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: sodium citrate, ammonium acetate, MPD, sodium chloride, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2001 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. all: 89378 / Num. obs: 89378 / % possible obs: 97 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / Num. unique all: 8488 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1JBM Resolution: 1.9→19.79 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: No NCS-restraints applied at any point in the refinement
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8996 Å2 / ksol: 0.339434 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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