[English] 日本語
Yorodumi- PDB-1j3a: Crystal structure of ribosomal protein L13 from Pyrococcus horikoshii -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j3a | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of ribosomal protein L13 from Pyrococcus horikoshii | ||||||
Components | 50S ribosomal protein L13P | ||||||
Keywords | RIBOSOME / ribosomal protein / rRNA binding / ribosomal assembly | ||||||
Function / homology | Function and homology information large ribosomal subunit / structural constituent of ribosome / translation Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Nakashima, T. / Tanaka, M. / Kazama, T. / Kawamura, S. / Kimura, M. / Yao, M. / Tanaka, I. | ||||||
Citation | Journal: To be Published Title: Crystal structure of ribosomal protein L13 from hyperthermophilic archaeon Pyrococcus horikoshii Authors: Nakashima, T. / Tanaka, M. / Kazama, T. / Kawamura, S. / Kimura, M. / Yao, M. / Tanaka, I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1j3a.cif.gz | 39.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1j3a.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 1j3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j3a_validation.pdf.gz | 361.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1j3a_full_validation.pdf.gz | 364 KB | Display | |
Data in XML | 1j3a_validation.xml.gz | 3.9 KB | Display | |
Data in CIF | 1j3a_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/1j3a ftp://data.pdbj.org/pub/pdb/validation_reports/j3/1j3a | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 16330.272 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Gene: PH1634 / Plasmid: pet22b / Production host: Escherichia coli (E. coli) / References: UniProt: O59300 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.87 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Phosphate-citrate, 20% PEG8000, 0.2M NaCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
---|---|
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→22.7 Å / Num. obs: 17561 / % possible obs: 94.8 % |
Reflection shell | Resolution: 1.6→1.69 Å / % possible all: 77.2 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→10 Å
| ||||||||||||||||||||
Refine LS restraints |
|