+Open data
-Basic information
Entry | Database: PDB / ID: 4lab | ||||||
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Title | Crystal structure of the catalytic domain of RluB | ||||||
Components | Ribosomal large subunit pseudouridine synthase B | ||||||
Keywords | RNA BINDING PROTEIN / beta sheet / alpha-beta protein / pseudouridine synthase / E. coli ribosomal RNA | ||||||
Function / homology | Function and homology information 23S rRNA pseudouridine2605 synthase / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5043 Å | ||||||
Authors | Czudnochowski, N. / Finer-Moore, J.S. / Stroud, R.M. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: The mechanism of pseudouridine synthases from a covalent complex with RNA, and alternate specificity for U2605 versus U2604 between close homologs. Authors: Czudnochowski, N. / Ashley, G.W. / Santi, D.V. / Alian, A. / Finer-Moore, J. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lab.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lab.ent.gz | 67.3 KB | Display | PDB format |
PDBx/mmJSON format | 4lab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/4lab ftp://data.pdbj.org/pub/pdb/validation_reports/la/4lab | HTTPS FTP |
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-Related structure data
Related structure data | 4lgtC 2gmlS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 28552.619 Da / Num. of mol.: 1 / Fragment: UNP Residues 1-251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1269, JW1261, rluB, yciL / Plasmid: pET47 modified / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P37765, 23S rRNA pseudouridine2605 synthase | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.23 Å3/Da / Density % sol: 44.74 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M tri-Sodium citrate pH 5.6, 20% isopropanol, 15% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.06883 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2011 / Details: monochromator |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.06883 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→58.259 Å / Num. all: 9324 / Num. obs: 9324 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 18.9 % / Biso Wilson estimate: 56.5 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 21.52 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 17.5 % / Rmerge(I) obs: 1.53 / Mean I/σ(I) obs: 2.6 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GML Resolution: 2.5043→58.259 Å / SU ML: 0.3 Isotropic thermal model: Isotropic with TLS parameters for 2 groups σ(F): 2 / Phase error: 31.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5043→58.259 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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