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Yorodumi- PDB-6ugi: Crystal structure of a fragment of E. coli tRNA(Asp) consisting o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ugi | |||||||||||||||
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Title | Crystal structure of a fragment of E. coli tRNA(Asp) consisting of its acceptor stem/T stem-loop. Long unit cell. | |||||||||||||||
Components | tRNA(Asp) acceptor stem/T stem-loop | |||||||||||||||
Keywords | RNA / tRNA RNA unmodified T-loop acceptor stem | |||||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||||||||
Authors | Chan, C.W. / Mondragon, A. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Rna / Year: 2020 Title: Crystal structures of an unmodified bacterial tRNA reveal intrinsic structural flexibility and plasticity as general properties of unbound tRNAs. Authors: Chan, C.W. / Badong, D. / Rajan, R. / Mondragon, A. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ugi.cif.gz | 30.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ugi.ent.gz | 19.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ugi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ugi_validation.pdf.gz | 413.4 KB | Display | wwPDB validaton report |
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Full document | 6ugi_full_validation.pdf.gz | 413 KB | Display | |
Data in XML | 6ugi_validation.xml.gz | 4.2 KB | Display | |
Data in CIF | 6ugi_validation.cif.gz | 5.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ug/6ugi ftp://data.pdbj.org/pub/pdb/validation_reports/ug/6ugi | HTTPS FTP |
-Related structure data
Related structure data | 6uggC 6ugjSC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: RNA chain | Mass: 9989.942 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / Details: 2 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K Ambient temp details: flash frozen with liquid nitrogen in crystallization well solution supplemented with either increased ammonium sulfate concentration or with 20% (v/v) glycerol for cryo-protection Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2018 / Details: Monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→37.38 Å / Num. obs: 9226 / % possible obs: 89 % / Redundancy: 8.1 % / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.045 / Rrim(I) all: 0.126 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.754→1.872 Å / Redundancy: 7.4 % / Rmerge(I) obs: 1.257 / Num. unique obs: 3401 / CC1/2: 0.683 / Rpim(I) all: 0.494 / Rrim(I) all: 1.354 / % possible all: 34.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6UGJ Resolution: 1.75→37.38 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.066 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.141 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.84 Å2 / Biso mean: 33.009 Å2 / Biso min: 17.78 Å2
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Refinement step | Cycle: final / Resolution: 1.75→37.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.752→1.798 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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