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Yorodumi- PDB-2dog: Solution structure of the N-terminal domain of RimM from Thermus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dog | ||||||
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Title | Solution structure of the N-terminal domain of RimM from Thermus thermophilus HB8 | ||||||
Components | Probable 16S rRNA-processing protein rimM | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information rRNA processing / ribosomal small subunit biogenesis / ribosome binding / ribosome / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | SOLUTION NMR / torsion angle dyanamics, simulated annealing | ||||||
Authors | Suzuki, S. / Matsumoto, E. / Tatsuguchi, A. / Kawazoe, M. / Kaminishi, T. / Takemoto, C. / Shirouzu, M. / Muto, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Bacteriol. / Year: 2007 Title: Structural characterization of the ribosome maturation protein, RimM Authors: Suzuki, S. / Tatsuguchi, A. / Matsumoto, E. / Kawazoe, M. / Kaminishi, T. / Shirouzu, M. / Muto, Y. / Takemoto, C. / Yokoyama, S. | ||||||
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 | 2dog.cif.gz | 518.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dog.ent.gz | 434.1 KB | Display | PDB format |
PDBx/mmJSON format | 2dog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/2dog ftp://data.pdbj.org/pub/pdb/validation_reports/do/2dog | 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: 9493.972 Da / Num. of mol.: 1 / Fragment: RIEF fold Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: rimM / Plasmid: PC011033-04 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SJH5 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.2mM 13C/15N-PROTEIN, 20mM sodium phosphate (pH6.5), 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dyanamics, simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |