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Yorodumi- PDB-1c06: SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c06 | ||||||
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Title | SOLUTION STRUCTURE OF RIBOSOMAL PROTEIN S4 DELTA 41, REFINED WITH DIPOLAR COUPLINGS (ENSEMBLE OF 16 STRUCTURES) | ||||||
Components | RIBOSOMAL PROTEIN S4 DELTA 41 | ||||||
Keywords | RIBOSOME / TWO SUBDOMAINS / UNIQUE TOPOLOGY / POSSIBLE HELIX-TURN HELIX MOTIF | ||||||
Function / homology | Function and homology information ribosomal small subunit biogenesis / small ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / response to antibiotic Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | SOLUTION NMR / HYBRID DGSA PROTOCOL WITHOUT THE DIPOLAR COUPLING RESTRAINTS, ADDITIONAL SA WITH THE DIPOLAR COUPLING RESTRAINTS ADDED | ||||||
Authors | Markus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases. Authors: Markus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A. #1: Journal: Embo J. / Year: 1998 Title: The solution structure of ribosomal protein S4 delta 41 reveals two subdomains and a positively charged surface that may interact with RNA Authors: Markus, M.A. / Gerstner, R.B. / Draper, D.E. / Torchia, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c06.cif.gz | 907.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c06.ent.gz | 767.1 KB | Display | PDB format |
PDBx/mmJSON format | 1c06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c06_validation.pdf.gz | 345.1 KB | Display | wwPDB validaton report |
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Full document | 1c06_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 1c06_validation.xml.gz | 59.5 KB | Display | |
Data in CIF | 1c06_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c06 ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c06 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 18624.359 Da / Num. of mol.: 1 / Fragment: S4 DELTA 41 (S4 RESIDUES 42-200) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: PET13A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P81288 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THESE STRUCTURES WERE DETERMINED WITH NOE RESTRAINTS FROM MULTIDIMENSIONAL HETERONUCLEAR EXPERIMENTS, DIHEDRAL ANGLE RESTRAINTS BASED ON MEASUREMENTS OF SCALAR COUPLING CONSTANTS, AND DIPOLAR ...Text: THESE STRUCTURES WERE DETERMINED WITH NOE RESTRAINTS FROM MULTIDIMENSIONAL HETERONUCLEAR EXPERIMENTS, DIHEDRAL ANGLE RESTRAINTS BASED ON MEASUREMENTS OF SCALAR COUPLING CONSTANTS, AND DIPOLAR COUPLING RESTRAINTS MEASURED ON SAMPLES IN PARTIALLY ALIGNED PHASES. THE STRUCTURES ARE ARRANGED IN ORDER FROM LOWEST TO HIGHEST X-PLOR ENERGY. |
-Sample preparation
Details |
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Sample conditions |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: HYBRID DGSA PROTOCOL WITHOUT THE DIPOLAR COUPLING RESTRAINTS, ADDITIONAL SA WITH THE DIPOLAR COUPLING RESTRAINTS ADDED Software ordinal: 1 Details: SUMMARY OF RESTRAINTS: 2170 NOE, 86 HYDROGEN BOND, 114 DIHEDRAL ANGLE, AND 101 DIPOLAR COUPLINGS | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 16 |