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Yorodumi- PDB-4bsz: Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bsz | ||||||
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Title | Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN | ||||||
Function / homology | Function and homology information : / : / SBF transcription complex / MBF transcription complex / chromatin => GO:0000785 / response to osmotic stress / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor ...: / : / SBF transcription complex / MBF transcription complex / chromatin => GO:0000785 / response to osmotic stress / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / DNA-(apurinic or apyrimidinic site) endonuclease activity / 90S preribosome / positive regulation of apoptotic signaling pathway / regulation of protein localization / unfolded protein binding / ribosomal small subunit biogenesis / cellular response to oxidative stress / cytosolic small ribosomal subunit / cytoplasmic translation / structural constituent of ribosome / RNA binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.842 Å | ||||||
Authors | Holzer, S. / Ban, N. / Klinge, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Crystal Structure of the Yeast Ribosomal Protein Rps3 in Complex with its Chaperone Yar1 Authors: Holzer, S. / Ban, N. / Klinge, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bsz.cif.gz | 147.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bsz.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bsz_validation.pdf.gz | 427.1 KB | Display | wwPDB validaton report |
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Full document | 4bsz_full_validation.pdf.gz | 429.5 KB | Display | |
Data in XML | 4bsz_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 4bsz_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/4bsz ftp://data.pdbj.org/pub/pdb/validation_reports/bs/4bsz | HTTPS FTP |
-Related structure data
Related structure data | 2j00 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26957.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: W303 / Plasmid: PRSF-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P05750 |
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#2: Protein | Mass: 22608.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: W303 / Plasmid: PRSF-DUET1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: P46683 |
Sequence details | THE CRYSTALLISED CONSTRUCT CONTAINS AN N-TERMINAL ADDITION OF THE RESIDUE SEQUENCE MADP AS A RESULT ...THE CRYSTALLIS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.19 % Description: SBGRID WIDE SEARCH MOLECULAR REPLACEMENT WSMR, STOKES-REES ET AL 2010, WAS USED AND THE STRUCTURE WAS SOLVED BY USING PHASER WITH THE FOLLOWING ENTRIES 2J00 - CHAIN C, N-TERMINAL DOMAIN 1MJ0A |
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Crystal grow | Details: 0.1 M MES PH 6.0, 200 MM LITHIUM SULPHATE, 20% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→34.57 Å / Num. obs: 12331 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 8.19130646 % / Biso Wilson estimate: 76.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.85 |
Reflection shell | Resolution: 2.84→3.01 Å / Redundancy: 8.41671018 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.86 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J00 2j00 Resolution: 2.842→34.574 Å / SU ML: 0.4 / σ(F): 2 / Phase error: 23.53 / Stereochemistry target values: ML Details: ABSENT REGIONS INCLUDE THE C-TERMINUS OF RPS3 AND THE C-TERMINUS OF YAR1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 79.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.842→34.574 Å
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Refine LS restraints |
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LS refinement shell |
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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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