+Open data
-Basic information
Entry | Database: PDB / ID: 2jq7 | ||||||||||||
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Title | Model for thiostrepton binding to the ribosomal L11-RNA | ||||||||||||
Components |
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Keywords | RIBOSOME/ANTIBIOTIC / RIBOSOME-ANTIBIOTIC COMPLEX / THIOPEPTIDE / ANTIBACTERIAL / THIAZOLE / THIAZOLINE / OXAZOLE / RIBOSOME / L11 / TRANSLATION INHIBITION | ||||||||||||
Function / homology | Function and homology information large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / structural constituent of ribosome / defense response to bacterium / translation / extracellular region Similarity search - Function | ||||||||||||
Biological species | THERMOTOGA MARITIMA (bacteria) STREPTOMYCES AZUREUS (bacteria) Escherichia coli (E. coli) | ||||||||||||
Method | SOLUTION NMR / DOCKING | ||||||||||||
Authors | Jonker, H.R.A. / Ilin, S. / Grimm, S.K. / Woehnert, J. / Schwalbe, H. | ||||||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2007 Title: L11 Domain Rearrangement Upon Binding to RNA and Thiostrepton Studied by NMR Spectroscopy Authors: Jonker, H.R.A. / Ilin, S. / Grimm, S.K. / Woehnert, J. / Schwalbe, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jq7.cif.gz | 470.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jq7.ent.gz | 401.1 KB | Display | PDB format |
PDBx/mmJSON format | 2jq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jq7_validation.pdf.gz | 399.9 KB | Display | wwPDB validaton report |
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Full document | 2jq7_full_validation.pdf.gz | 574.6 KB | Display | |
Data in XML | 2jq7_validation.xml.gz | 49.6 KB | Display | |
Data in CIF | 2jq7_validation.cif.gz | 62.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/2jq7 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/2jq7 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: IPAP(1H, 15N)HSQC |
NMR details | Text: THE RDC DATA WAS USED TO DETERMINE THE RELATIVE DOMAIN ORIENTATION OF THE L11 PROTEIN |
-Sample preparation
Details | Type: solution Contents: 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O Label: sample_1 / Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 220 / pH: 6.1 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE DRX / Manufacturer: Bruker / Model: AVANCE DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: DOCKING / Software ordinal: 1 Details: FOR CHAIN A, THE INITIAL COORDINATES ARE OPTIMIZED USING RDCS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE ...Details: FOR CHAIN A, THE INITIAL COORDINATES ARE OPTIMIZED USING RDCS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN B, INITIAL T. MARITIMA COORDINATES ARE FROM PDB ENTRY 1MMS. LEFT SEMI-FLEXIBLE DURING DOCKING. FOR CHAIN C, THE INITIAL COORDINATES ARE FROM PDB ENTRY 1E9W. LEFT FLEXIBLE ACIDS AND NUCLEIC ACIDS WHICH DO NOT COMPLY WELL WITH THE ANTIBIOTIC IN THE CASE HERE. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: TOP-RANKED ENSEMBLE, ACCORDING TO THE AVERAGE INTERACTION ENERGY AND BURIED SURFACE AREA Conformers calculated total number: 200 / Conformers submitted total number: 10 |