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Yorodumi- PDB-2kjv: Solution structure and backbone dynamics of the ribosomal protein S6wt -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kjv | ||||||
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Title | Solution structure and backbone dynamics of the ribosomal protein S6wt | ||||||
Components | 30S ribosomal protein S6 | ||||||
Keywords | RIBOSOMAL PROTEIN / S6 / solution structure / backbone dynamics / folding / Ribonucleoprotein / RNA-binding / rRNA-binding | ||||||
Function / homology | Function and homology information rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Ohman, A. / Oliveberg, M. / Oman, T. | ||||||
Citation | Journal: Protein Sci. / Year: 2010 Title: Solution structures and backbone dynamics of the ribosomal protein S6 and its permutant P(54-55) Authors: Ohman, A. / Oman, T. / Oliveberg, M. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: The HD-exchange motions of ribosomal protein S6 are insensitive to reversal of the protein-folding pathway Authors: Haglund, E. / Lind, J. / Oman, T. / Ohman, A. / Maler, L. / Oliveberg, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kjv.cif.gz | 664.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kjv.ent.gz | 553.6 KB | Display | PDB format |
PDBx/mmJSON format | 2kjv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kjv_validation.pdf.gz | 349.1 KB | Display | wwPDB validaton report |
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Full document | 2kjv_full_validation.pdf.gz | 545.8 KB | Display | |
Data in XML | 2kjv_validation.xml.gz | 47.3 KB | Display | |
Data in CIF | 2kjv_validation.cif.gz | 71.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kj/2kjv ftp://data.pdbj.org/pub/pdb/validation_reports/kj/2kjv | HTTPS FTP |
-Related structure data
Related structure data | 2kjwC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11988.753 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: rpsF, rps6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): pLysS / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Solution structure and backbone dynamics of the ribosomal protein S6wt | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | pH: 6.3 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: sa.inp and refine.inp used with slight modifications. | ||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 745 / NOE intraresidue total count: 252 / NOE long range total count: 89 / NOE medium range total count: 97 / NOE sequential total count: 307 / Protein phi angle constraints total count: 90 / Protein psi angle constraints total count: 65 | ||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 300 / Conformers submitted total number: 20 |