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Yorodumi- PDB-1dfu: CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dfu | ||||||
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Title | CRYSTAL STRUCTURE OF E.COLI RIBOSOMAL PROTEIN L25 COMPLEXED WITH A 5S RRNA FRAGMENT AT 1.8 A RESOLUTION | ||||||
Components |
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Keywords | RIBOSOME / PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information ribosomal large subunit assembly / response to radiation / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / negative regulation of translation / structural constituent of ribosome / translation / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | ||||||
Authors | Lu, M. / Steitz, T.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution. Authors: Lu, M. / Steitz, T.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dfu.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dfu.ent.gz | 41.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dfu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dfu_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
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Full document | 1dfu_full_validation.pdf.gz | 454.7 KB | Display | |
Data in XML | 1dfu_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 1dfu_validation.cif.gz | 15.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1dfu ftp://data.pdbj.org/pub/pdb/validation_reports/df/1dfu | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 6155.753 Da / Num. of mol.: 1 / Fragment: LOOP E-HELIX IV FRAGMENT / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E.COLI | ||
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#2: RNA chain | Mass: 6206.706 Da / Num. of mol.: 1 / Fragment: LOOP E-HELIX IV FRAGMENT / Source method: obtained synthetically / Details: THIS SEQUENCE OCCURS NATURALLY IN E.COLI | ||
#3: Protein | Mass: 10713.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: PROTEIN FROM THE LARGE RIBOSOMAL SUBUNIT / Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PL25 / Production host: Escherichia coli (E. coli) / References: UniProt: P68919 | ||
#4: Chemical | ChemComp-MG / #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: 2.98 Å3/Da / Density % sol: 58.76 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: MPD, POTASSIUM CHLORIDE, MAGNESIUM CHLORIDE, CACODYLATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP at 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X12C / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 24727 / % possible obs: 96 % / Observed criterion σ(I): 2.9 / Redundancy: 15 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 5 % / Rmerge(I) obs: 0.313 / % possible all: 77 |
Reflection shell | *PLUS % possible obs: 77 % / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(I): 2 / Stereochemistry target values: CNS
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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