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Yorodumi- PDB-1r3e: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r3e | ||||||
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Title | Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit | ||||||
Components |
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Keywords | LYASE/RNA / RNA modification / pseudouridylation / LYASE-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å | ||||||
Authors | Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA Recognition Through a Combination of Rigid Docking and Induced Fit Authors: Pan, H. / Agarwalla, S. / Moustakas, D.T. / Finer-Moore, J. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r3e.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r3e.ent.gz | 83.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r3e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/1r3e ftp://data.pdbj.org/pub/pdb/validation_reports/r3/1r3e | HTTPS FTP |
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-Related 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: 5416.227 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: RNA chain | Mass: 5380.221 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | | Mass: 35516.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TRUB / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9WZW0, pseudouridylate synthase #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, magnesium sulfate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9730, 0.9796, 0.9800, 1.1271 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.1→15 Å / Num. all: 39270 / Num. obs: 38642 / % possible obs: 98.4 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15 | |||||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 97.5 | |||||||||||||||
Reflection | *PLUS Num. measured all: 525236 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.731 / Mean I/σ(I) obs: 45.3 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.1→15 Å / σ(F): 2.1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→15 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Num. reflection obs: 34732 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |