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Yorodumi- PDB-1p6v: Crystal structure of the tRNA domain of transfer-messenger RNA in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p6v | ||||||
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Title | Crystal structure of the tRNA domain of transfer-messenger RNA in complex with SmpB | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / SmpB / tmRNA / trans-translation / protein-RNA complex / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å | ||||||
Authors | Gutmann, S. / Haebel, P.W. / Metzinger, L. / Sutter, M. / Felden, B. / Ban, N. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB Authors: Gutmann, S. / Haebel, P.W. / Metzinger, L. / Sutter, M. / Felden, B. / Ban, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p6v.cif.gz | 93.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p6v.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 1p6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p6v_validation.pdf.gz | 470.9 KB | Display | wwPDB validaton report |
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Full document | 1p6v_full_validation.pdf.gz | 504.6 KB | Display | |
Data in XML | 1p6v_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1p6v_validation.cif.gz | 24 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p6v ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p6v | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | SmpB (chain A) and tmRNA[delta] (chain B) for the ribonucleoprotein complex / SmpB (chain C) and tmRNA[delta] (chain D) for the ribonucleoprotein complex; poorer defined in electron density |
-Components
#1: RNA chain | Mass: 21959.070 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: In vitro transcription of Aquifex aeolicus tmRNA[delta] #2: Protein | Mass: 18440.818 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: SMPB / Production host: Escherichia coli (E. coli) / References: UniProt: O66640 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.22 Å3/Da / Density % sol: 76.25 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: Isopropanol, cacodylate, ammonium acetate, magnesium acetate, calcium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.008 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 12, 2002 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.008 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 17756 / Num. obs: 17756 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.07 / Net I/σ(I): 23.1 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.87 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.873 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 3.2→19.94 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: GROUPED B-Factors / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 90.774 Å2 / ksol: 0.224974 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 108.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.2→19.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.2 Å / Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.36 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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