+Open data
-Basic information
Entry | Database: PDB / ID: 2oml | ||||||
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Title | crystal structure of E. coli pseudouridine synthase RluE | ||||||
Components | Ribosomal large subunit pseudouridine synthase E | ||||||
Keywords | ISOMERASE / bifurcated beta sheet / thrombin-cleaved | ||||||
Function / homology | Function and homology information 23S rRNA pseudouridine2457 synthase / 23S rRNA pseudouridine(2457) synthase activity / maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) / maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Pan, H. / Ho, J.D. / Stroud, R.M. / Finer-Moore, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: The Crystal Structure of E. coli rRNA Pseudouridine Synthase RluE. Authors: Pan, H. / Ho, J.D. / Stroud, R.M. / Finer-Moore, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oml.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oml.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 2oml.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oml_validation.pdf.gz | 433.9 KB | Display | wwPDB validaton report |
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Full document | 2oml_full_validation.pdf.gz | 434.9 KB | Display | |
Data in XML | 2oml_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 2oml_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/2oml ftp://data.pdbj.org/pub/pdb/validation_reports/om/2oml | HTTPS FTP |
-Related structure data
Related structure data | 2olwC 1ksvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biologically active protein is a monomer |
-Components
#1: Protein | Mass: 21440.342 Da / Num. of mol.: 1 / Fragment: catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluE / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P75966, Isomerases; Intramolecular transferases; Transferring other groups | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 1.95 Å3/Da / Density % sol: 36.98 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by ...Details: 4 mg/ml protein in 10 mM Tris, pH 7.5, 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate, crystals were improved by microseeding a solution of 18-22% MME PEG 2000, 200 mM ammonium sulfate, 100 mM sodium acetate and 2 mg/ml protein at pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.954 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 2, 2003 / Details: double crystal monochrometer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 13.7 / Number: 241836 / Rmerge(I) obs: 0.063 / Χ2: 1.12 / D res high: 1.2 Å / D res low: 40 Å / Num. obs: 52181 / % possible obs: 98.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.2→40 Å / Num. obs: 52181 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 10.3 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.125 / Net I/σ(I): 13.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4929 / Χ2: 1.277 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1KSV with N-terminal domain removed Resolution: 1.2→28.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.2 / SU ML: 0.024 Isotropic thermal model: restrained individual anisotropic B-factor refinement Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.043 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→28.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.233 Å / Total num. of bins used: 20
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