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Yorodumi- PDB-3jq4: The structure of the complex of the large ribosomal subunit from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jq4 | ||||||
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Title | The structure of the complex of the large ribosomal subunit from D. Radiodurans with the antibiotic lankacidin | ||||||
Components |
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Keywords | RNA / Ribosome structure / antibiotics / lankacidin / lankamycin / protein synthesis / inhibitors / synergism / macrolide | ||||||
Function / homology | Chem-LC2 / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | ||||||
Biological species | Deinococcus radiodurans (radioresistant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.52 Å | ||||||
Authors | Auerbach-Nevo, T. / Mermershtain, I. / Davidovich, C. / Bashan, A. / Rozenberg, H. / Yonath, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics Authors: Auerbach, T. / Mermershtain, I. / Davidovich, C. / Bashan, A. / Belousoff, M. / Wekselman, I. / Zimmerman, E. / Xiong, L. / Klepacki, D. / Arakawa, K. / Kinashi, H. / Mankin, A.S. / Yonath, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jq4.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3jq4.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 3jq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jq4_validation.pdf.gz | 735.7 KB | Display | wwPDB validaton report |
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Full document | 3jq4_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3jq4_validation.xml.gz | 87.9 KB | Display | |
Data in CIF | 3jq4_validation.cif.gz | 140.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/3jq4 ftp://data.pdbj.org/pub/pdb/validation_reports/jq/3jq4 | HTTPS FTP |
-Related structure data
Related structure data | 1nkwS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: RNA chain | Mass: 933405.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / Strain: R1 / References: GenBank: 11612676 |
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#2: RNA chain | Mass: 38029.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinococcus radiodurans (radioresistant) / Strain: R1 / References: GenBank: 11612676 |
#3: Chemical | ChemComp-LC2 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.98 Å3/Da / Density % sol: 64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: ETHANOL, DIMETHYL HEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 3.5→40 Å / Num. all: 293734 / Num. obs: 271411 / % possible obs: 92.4 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.163 / Net I/σ(I): 7.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1NKW Resolution: 3.52→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 11982034.28 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): -2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: -12.7962 Å2 / ksol: 0.15 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 111.5 Å2
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Refinement step | Cycle: LAST / Resolution: 3.52→8 Å
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Refine LS restraints |
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Xplor file |
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