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Yorodumi- PDB-1prz: Crystal structure of pseudouridine synthase RluD catalytic module -
+Open data
-Basic information
Entry | Database: PDB / ID: 1prz | ||||||
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Title | Crystal structure of pseudouridine synthase RluD catalytic module | ||||||
Components | Ribosomal large subunit pseudouridine synthase D | ||||||
Keywords | LYASE / Pseudouridine synthase / RluD / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | Function and homology information 23S rRNA pseudouridine1911/1915/1917 synthase / 23S rRNA pseudouridine(1911/1915/1917) synthase activity / rRNA pseudouridine synthase activity / pseudouridine synthesis / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / rRNA processing / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MAD / Resolution: 1.8 Å | ||||||
Authors | Sivaraman, J. / Iannuzzi, P. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Crystal structure of the RluD pseudouridine Synthase catalytic module, an enzyme that modifies 23S rRNA and is essential for normal cell growth of Escherichia coli Authors: Sivaraman, J. / Iannuzzi, P. / Cygler, M. / Matte, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1prz.cif.gz | 65 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1prz.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 1prz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1prz_validation.pdf.gz | 419.7 KB | Display | wwPDB validaton report |
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Full document | 1prz_full_validation.pdf.gz | 424.4 KB | Display | |
Data in XML | 1prz_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 1prz_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/1prz ftp://data.pdbj.org/pub/pdb/validation_reports/pr/1prz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29229.068 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RLUD or SFHB / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 References: UniProt: Q8X9F0, UniProt: P33643*PLUS, pseudouridylate synthase |
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#2: 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: 2.64 Å3/Da / Density % sol: 53 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 7 Details: PEG 8000, KCL, Glycerol, pH 7., microbatch under oil, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: batch method | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Feb 24, 2003 |
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 32444 / Num. obs: 32444 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Rsym value: 0.065 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 98.3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. measured all: 107285 / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 45 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |