+Open data
-Basic information
Entry | Database: PDB / ID: 1emi | ||||||
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Title | STRUCTURE OF 16S RRNA IN THE REGION AROUND RIBOSOMAL PROTEIN S8. | ||||||
Components |
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Keywords | RIBOSOME / RNA / rRNA / ribosomal protein / 16S rRNA / S8 | ||||||
Function / homology | Function and homology information cytosolic small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 7.5 Å | ||||||
Authors | Lancaster, L. / Culver, G.M. / Yusupova, G.Z. / Cate, J.H. / Yuspov, M.M. / Noller, H.F. | ||||||
Citation | Journal: RNA / Year: 2000 Title: The location of protein S8 and surrounding elements of 16S rRNA in the 70S ribosome from combined use of directed hydroxyl radical probing and X-ray crystallography. Authors: Lancaster, L. / Culver, G.M. / Yusupova, G.Z. / Cate, J.H. / Yusupov, M.M. / Noller, H.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1emi.cif.gz | 22.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1emi.ent.gz | 10.5 KB | Display | PDB format |
PDBx/mmJSON format | 1emi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1emi_validation.pdf.gz | 306.9 KB | Display | wwPDB validaton report |
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Full document | 1emi_full_validation.pdf.gz | 306.9 KB | Display | |
Data in XML | 1emi_validation.xml.gz | 795 B | Display | |
Data in CIF | 1emi_validation.cif.gz | 3.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/1emi ftp://data.pdbj.org/pub/pdb/validation_reports/em/1emi | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 51921.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: COORDINATES FOR THERMUS THERMOPHILUS 16S RRNA BUT SEQUENCE AND NUMBERING IS THAT OF E.COLI 16S RRNA Source: (natural) Thermus thermophilus (bacteria) |
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#2: Protein | Mass: 15624.214 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: Q5SHQ2, UniProt: P0DOY9*PLUS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal grow | *PLUS Method: unknown |
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-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 1.1051 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1051 Å / Relative weight: 1 |
Reflection | Highest resolution: 7.5 Å |
-Processing
Software |
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Refinement | Highest resolution: 7.5 Å Details: All data collection parameters are as reported for 486D. The RNA model for the S8 region of 16S rRNA was built manually by fitting to the 7.8 A X-ray map of the Thermus thermophilus 70S ...Details: All data collection parameters are as reported for 486D. The RNA model for the S8 region of 16S rRNA was built manually by fitting to the 7.8 A X-ray map of the Thermus thermophilus 70S ribosome (Cate et al., Science 285, 2095-2104, 1999; see PDB 486D) using a single P pseudoatom for each nucleotide. Note that the nucleotide numbering corresponds to the nucleotide positions of E.coli 16S rRNA. Protein S8 from Thermus thermophilus (PDB 1AN7) was fitted to the 7.8 A map of the Thermus thermophilus 70S ribosome by splitting the protein into N- and C-terminal domains between residues 80 and 81. The two domains were fit separately, resulting in a small relative movement compared with the original X-ray structure. Only C-alpha positions are given in the PDB file. | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 7.5 Å
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