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Yorodumi- PDB-4lq4: crystal structure of mutant ribosomal protein L1 from Methanococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lq4 | ||||||
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Title | crystal structure of mutant ribosomal protein L1 from Methanococcus jannaschii with deletion of 8 residues from C-terminus | ||||||
Components | 50S ribosomal protein L1 | ||||||
Keywords | RIBOSOMAL PROTEIN / Beta-Alpha-Beta / structural constituent of ribosome / rRNA binding / regulation of translation / translation / Ribosomal RNA / mRNA | ||||||
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 | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Gabdulkhakov, A.G. / Tishchenko, S.V. / Shkliaeva, A.A. / Garber, M.B. / Nikonov, S.V. / Sarskikh, A.V. | ||||||
Citation | Journal: Crystallography Reports / Year: 2014 Title: Crystal structure of a mutant of archaeal ribosomal protein L1 from Methanococcus jannaschii Authors: Sarskikh, A.V. / Gabdulkhakov, A.G. / Kostareva, O.S. / Shkliaeva, A.A. / Tishchenko, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lq4.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lq4.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 4lq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lq4_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 4lq4_full_validation.pdf.gz | 429.6 KB | Display | |
Data in XML | 4lq4_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 4lq4_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lq/4lq4 ftp://data.pdbj.org/pub/pdb/validation_reports/lq/4lq4 | HTTPS FTP |
-Related structure data
Related structure data | 1i2aS S: Starting model for refinement |
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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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Details | part of ribosome |
-Components
#1: Protein | Mass: 23867.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ0510, rpl1, rplA / Plasmid: pET11a-PL-MjaL1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54050 | ||
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#2: Chemical | ChemComp-TLA / | ||
#3: Chemical | ChemComp-IPA / | ||
#4: Chemical | #5: 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: 2.79 Å3/Da / Density % sol: 55.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG4000, 10% isopropanol, 0.1 M Hepes-NaOH, 0.5 mkl 0.8 KNa-tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54189 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 27, 2010 |
Radiation | Monochromator: Montel 200 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54189 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→40 Å / Num. all: 26394 / Num. obs: 26074 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.34 Å2 |
Reflection shell | Resolution: 1.75→1.85 Å / % possible all: 93.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I2A Resolution: 1.75→32.86 Å / SU ML: 0.2 / σ(F): 1.19 / Phase error: 21.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→32.86 Å
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Refine LS restraints |
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LS refinement shell |
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