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Yorodumi- PDB-1xpi: Crystal structure of the catalytic domain of E. coli pseudouridin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xpi | ||||||
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Title | Crystal structure of the catalytic domain of E. coli pseudouridine synthase RluC | ||||||
Components | Ribosomal large subunit pseudouridine synthase C | ||||||
Keywords | LYASE / PSEUDOURIDINE SYNTHASE / RLUC / CATALYTIC DOMAIN | ||||||
Function / homology | Function and homology information 23S rRNA pseudouridine955/2504/2580 synthase / 23S rRNA pseudouridine(955/2504/2580) synthase activity / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Del Campo, M. / Ofengand, J. / Fenna, R. / Malhotra, A. | ||||||
Citation | Journal: To be Published Title: Possible RNA binding domains of RluC and RluD Authors: Del Campo, M. / Ofengand, J. / Fenna, R. / Malhotra, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xpi.cif.gz | 105.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xpi.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 1xpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xpi_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 1xpi_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 1xpi_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 1xpi_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xp/1xpi ftp://data.pdbj.org/pub/pdb/validation_reports/xp/1xpi | HTTPS FTP |
-Related structure data
Related structure data | 1v9kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a monomer from the two molecules in the asymmetric unit. |
-Components
#1: Protein | Mass: 26010.869 Da / Num. of mol.: 2 / Fragment: sequence database residues 89-319 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluC / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AA39, pseudouridylate synthase #2: Chemical | ChemComp-ACY / #3: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.69 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Bicine, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 1998 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 24381 / Num. obs: 24381 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V9K (molecule A) Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.735 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.656 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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