+Open data
-Basic information
Entry | Database: PDB / ID: 1r5b | ||||||
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Title | Crystal structure analysis of sup35 | ||||||
Components | Eukaryotic peptide chain release factor GTP-binding subunit | ||||||
Keywords | TRANSLATION / TRANSLATION TERMINATION / PEPTIDE RELEASE / GTPASE | ||||||
Function / homology | Function and homology information Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytoplasmic translational termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity ...Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytoplasmic translational termination / translation release factor complex / translation release factor activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / GTP binding / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å | ||||||
Authors | Kong, C. / Song, H. | ||||||
Citation | Journal: Mol.Cell / Year: 2004 Title: Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe Authors: Kong, C. / Ito, K. / Walsh, M.A. / Wada, M. / Liu, Y. / Kumar, S. / Barford, D. / Nakamura, Y. / Song, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r5b.cif.gz | 96.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r5b.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 1r5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/1r5b ftp://data.pdbj.org/pub/pdb/validation_reports/r5/1r5b | HTTPS FTP |
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-Related 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: 52103.195 Da / Num. of mol.: 1 / Fragment: residues 196-662 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Gene: SUP35, SPCC584.04 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: O74718 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 59.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, Ethylene Glycol, PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9787, 0.9724, 0.9791 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 12, 2003 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.35→20 Å / Num. all: 28714 / Num. obs: 24790 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 11.2 | ||||||||||||
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / Num. unique all: 2840 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU B: 9.427 / SU ML: 0.209 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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