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- PDB-1prz: Crystal structure of pseudouridine synthase RluD catalytic module -
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Open data
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Basic information
Entry | Database: PDB / ID: 1prz | ||||||
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Title | Crystal structure of pseudouridine synthase RluD catalytic module | ||||||
![]() | Ribosomal large subunit pseudouridine synthase D | ||||||
![]() | LYASE / Pseudouridine synthase / RluD / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Sivaraman, J. / Iannuzzi, P. / Cygler, M. / Matte, A. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI) | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65 KB | Display | ![]() |
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PDB format | ![]() | 51.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() References: UniProt: Q8X9F0, UniProt: P33643*PLUS, pseudouridylate synthase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |