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Yorodumi- PDB-1lnx: Crystal structure of the P.aerophilum SmAP1 heptamer in a new cry... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lnx | ||||||
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Title | Crystal structure of the P.aerophilum SmAP1 heptamer in a new crystal form (C2221) | ||||||
Components | small nuclear ribonucleoprotein homolog (Sm-like) | ||||||
Keywords | RNA BINDING PROTEIN / transcription / beta barrel-like structure (OB fold) / homoheptameric | ||||||
Function / homology | Function and homology information pICln-Sm protein complex / mRNA splicing, via spliceosome / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Pyrobaculum aerophilum (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 | 1lnx.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lnx.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lnx_validation.pdf.gz | 517.7 KB | Display | wwPDB validaton report |
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Full document | 1lnx_full_validation.pdf.gz | 540.3 KB | Display | |
Data in XML | 1lnx_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 1lnx_validation.cif.gz | 37.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/1lnx ftp://data.pdbj.org/pub/pdb/validation_reports/ln/1lnx | HTTPS FTP |
-Related structure data
Related structure data | 1jbmC 1jriC 1lojC 1i8fS 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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Components on special symmetry positions |
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Details | The asymmetric unit contains the likely biologically relevant oligomer (heptamer). A 14-mer may be important, and is created by one of the crystallographic 2-folds (x, -y, -z). |
-Components
#1: Protein | Mass: 8937.272 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: SmAP1, GPA2549 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8ZYG5 #2: Chemical | ChemComp-URI / #3: Chemical | ChemComp-GOL / #4: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 Details: sodium acetate, ammonium acetate, PEG 4000, glycerol, uridine-5'-monophosphate, dithiothreitol, pH 8.2, VAPOR DIFFUSION, HANGING DROP at 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2001 / Details: Osmic 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: 2.05→100 Å / Num. all: 40722 / Num. obs: 40722 / % possible obs: 97.4 % / Observed criterion σ(F): -1.73 / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 4.1 / Num. unique all: 3949 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I8F Resolution: 2.05→19.78 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.3041 Å2 / ksol: 0.357027 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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