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Yorodumi- PDB-1dd4: Crystal structure of ribosomal protein l12 from thermotoga maritim -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dd4 | ||||||
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Title | Crystal structure of ribosomal protein l12 from thermotoga maritim | ||||||
Components | (50S RIBOSOMAL PROTEIN L7/L12) x 2 | ||||||
Keywords | RIBOSOME / DIMER FORMATION / FLEXIBILITY / HINGE REGION / FOUR-HELIX-BUNDLE / FIVE-HELIX- BUNDLE / ALPHA-BETA STRUCTURE / HELICAL HAIRPIN / DOMAINS | ||||||
Function / homology | Function and homology information cytosolic large ribosomal subunit / structural constituent of ribosome / translation / mRNA binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Wahl, M.C. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. | ||||||
Citation | Journal: Embo J. / Year: 2000 Title: Flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein L12. Authors: Wahl, M.C. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dd4.cif.gz | 78.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dd4.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 1dd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dd4_validation.pdf.gz | 414.1 KB | Display | wwPDB validaton report |
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Full document | 1dd4_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 1dd4_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 1dd4_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1dd4 ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1dd4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 13475.498 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29396 #2: Protein/peptide | Mass: 4260.978 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermotoga maritima (bacteria) / References: UniProt: P29396 #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.46 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 3.23M AMMONIUM SULFATE, 0.1M CITRATE, 7% (V/V) POLYETHYLENE GLYCOL 200, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||
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: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.25 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.25 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→16 Å / Num. all: 21795 / Num. obs: 19877 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 65.8 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.166 / % possible all: 93.7 |
Reflection | *PLUS Redundancy: 6.5 % |
Reflection shell | *PLUS % possible obs: 93.7 % / Mean I/σ(I) obs: 2.1 |
-Processing
Software |
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Refinement | Resolution: 2.4→8 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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