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Yorodumi- PDB-2i82: Crystal structure of pseudouridine synthase RluA: indirect sequen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i82 | ||||||
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Title | Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure | ||||||
Components |
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Keywords | Lyase/RNA / pseudouridine synthase / Lyase-RNA COMPLEX | ||||||
Function / homology | Function and homology information tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase / rRNA pseudouridine synthase activity / rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / RNA modification / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity ...tRNA pseudouridine32 synthase / 23S rRNA pseudouridine746 synthase / rRNA pseudouridine synthase activity / rRNA pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / RNA modification / tRNA pseudouridine synthase activity / pseudouridine synthesis / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA processing / rRNA processing / RNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å | ||||||
Authors | Hoang, C. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure Authors: Hoang, C. / Chen, J. / Vizthum, C.A. / Kandel, J.M. / Hamilton, C.S. / Mueller, E.G. / Ferre-D'Amare, A.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i82.cif.gz | 230.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i82.ent.gz | 187.2 KB | Display | PDB format |
PDBx/mmJSON format | 2i82.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/2i82 ftp://data.pdbj.org/pub/pdb/validation_reports/i8/2i82 | HTTPS FTP |
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-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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3 |
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4 |
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Unit cell |
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Details | The crystallographic model consists of all residues for the four RNA molecules in the asymmetric unit. |
-Components
#1: RNA chain | Mass: 6642.013 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Protein | Mass: 25083.588 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluA / Plasmid: pET15-b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P0AA37, pseudouridylate synthase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.45 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 25% PEG4000, 100mM Tris-HCl pH 8.5, 25mM MgCl2, 100mM LiCl, 1mM spermine, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 Wavelength: 0.9001, 0.92035, 0.92014, 0.942411, 0.979877, 0.979647 | |||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2005 | |||||||||||||||||||||
Radiation | Monochromator: Double crystal, Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.05→19.83 Å / Num. obs: 82366 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4.84 / Redundancy: 7.43 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 35.8 | |||||||||||||||||||||
Reflection shell | Resolution: 2.05→2.18 Å / Redundancy: 6.96 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 4.84 / Num. unique all: 8090 / Rsym value: 0.467 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.05→19.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2402292.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 47.5999 Å2 / ksol: 0.344821 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→19.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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