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Yorodumi- PDB-1wki: solution structure of ribosomal protein L16 from thermus thermoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wki | ||||||
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Title | solution structure of ribosomal protein L16 from thermus thermophilus HB8 | ||||||
Components | LSU ribosomal protein L16P | ||||||
Keywords | RIBOSOME / MIXED ALPHA/BETA / structural genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing, torsion angle dynamics | ||||||
Authors | Nishimura, M. / Yoshida, T. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S. / Ohkubo, T. / Kobayashi, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Solution Structure of Ribosomal Protein L16 from Thermus thermophilus HB8 Authors: Nishimura, M. / Yoshida, T. / Shirouzu, M. / Terada, T. / Kuramitsu, S. / Yokoyama, S. / Ohkubo, T. / Kobayashi, Y. | ||||||
History |
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Remark 650 | HELIX determination method: author determined | ||||||
Remark 700 | SHEET determination method: author determined |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1wki.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1wki.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 1wki.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/1wki ftp://data.pdbj.org/pub/pdb/validation_reports/wk/1wki | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15993.909 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: RPLP / Plasmid: PET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60489 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 100mM NACL / pH: 5.4 / Pressure: 1 atm / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, torsion angle dynamics / Software ordinal: 1 Details: The structure are based on a total of 2590 restraints, 2364 are noe-derived distance constraints, 162 dihedral angle restraints, 64 distance restraints from hydrogen bonds. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 700 / Conformers submitted total number: 30 |