+Open data
-Basic information
Entry | Database: PDB / ID: 1mzp | ||||||
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Title | Structure of the L1 protuberance in the ribosome | ||||||
Components |
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Keywords | RIBOSOME / ribosomal protein / RNA-protein complex | ||||||
Function / homology | Function and homology information regulation of translation / cytosolic large ribosomal subunit / tRNA binding / rRNA binding / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Sulfolobus acidocaldarius (acidophilic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.65 Å | ||||||
Authors | Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Zimmermann, R. ...Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Zimmermann, R. / Garber, M. / Nikonov, S. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of the L1 protuberance in the ribosome. Authors: Nikulin, A. / Eliseikina, I. / Tishchenko, S. / Nevskaya, N. / Davydova, N. / Platonova, O. / Piendl, W. / Selmer, M. / Liljas, A. / Drygin, D. / Zimmermann, R. / Garber, M. / Nikonov, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mzp.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mzp.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mzp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mzp_validation.pdf.gz | 453.6 KB | Display | wwPDB validaton report |
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Full document | 1mzp_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 1mzp_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1mzp_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mz/1mzp ftp://data.pdbj.org/pub/pdb/validation_reports/mz/1mzp | 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: 17836.684 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: Synthesis of the RNA fragment from the plasmid pDD55; sequence from cell-free(in vitro) system without living organism. | ||
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#2: Protein | Mass: 24690.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic) Description: AUTHOR STATES TO AVOID THE POTENTIAL MISINCORPORATION OF LYSINE INSTEAD OF ARGININE, THE HOST STRAIN WAS COTRANSFORMED WITH PUBS520, A PLASMID CARRYING THE GENE FOR TRNA(ARG)AGA-AGG. Plasmid: pSacL1.4 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P35024 | ||
#3: Chemical | #4: 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: 3.78 Å3/Da / Density % sol: 67.2 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG400, Tris HCl, KCl, MgCl2, ph 8.5, VAPOR DIFFUSION, HANGING DROP at 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7A / Wavelength: 0.9762,0.9330 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 28, 2002 | |||||||||
Radiation | Monochromator: Double crystal focusing monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.65→25 Å / Num. all: 22839 / Num. obs: 22839 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 70 Å2 / Rmerge(I) obs: 0.057 | |||||||||
Reflection shell | Resolution: 2.65→2.7 Å / Rmerge(I) obs: 0.376 / % possible all: 97.2 | |||||||||
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 35675 / Num. measured all: 277313 | |||||||||
Reflection shell | *PLUS % possible obs: 97.2 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.65→25 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1263310.5 / Data cutoff high rms absF: 1263310.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.521 Å2 / ksol: 0.32442 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.65→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.65→2.74 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 10
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Xplor file |
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Refinement | *PLUS Lowest resolution: 25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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