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Yorodumi- PDB-2c1w: The structure of XendoU: a splicing independent snoRNA processing... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c1w | ||||||
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Title | The structure of XendoU: a splicing independent snoRNA processing endoribonuclease | ||||||
Components | ENDOU PROTEIN | ||||||
Keywords | NUCLEASE / SNORNA / ENDORIBONUCLEASE / SPLICING INDEPENDENT PROCESSING | ||||||
Function / homology | Function and homology information sno(s)RNA processing / RNA endonuclease activity / manganese ion binding / Hydrolases; Acting on ester bonds / RNA binding / nucleus Similarity search - Function | ||||||
Biological species | XENOPUS LAEVIS (African clawed frog) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å | ||||||
Authors | Renzi, F. / Caffarelli, E. / Laneve, P. / Bozzoni, I. / Brunori, M. / Vallone, B. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2006 Title: The Structure of the Endoribonuclease Xendou: From Small Nucleolar RNA Processing to Severe Acute Respiratory Syndrome Coronavirus Replication. Authors: Renzi, F. / Caffarelli, E. / Laneve, P. / Bozzoni, I. / Brunori, M. / Vallone, B. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c1w.cif.gz | 349 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c1w.ent.gz | 299.1 KB | Display | PDB format |
PDBx/mmJSON format | 2c1w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/2c1w ftp://data.pdbj.org/pub/pdb/validation_reports/c1/2c1w | HTTPS FTP |
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-Related structure data
Related structure data | 2c09 |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 33905.223 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: Q8JFY9 #2: Chemical | #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: 2.4 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 5.5 Details: 1.6M AMMONIUM SULPHATE, 0.2M PHOSPHATE BUFFER PH5.5, pH 5.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 64530 / % possible obs: 96 % / Observed criterion σ(I): 4 / Redundancy: 4.3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.884 / Cross valid method: THROUGHOUT / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 45-53, 290-292 FROM ALL THREE NCS MONOMERS AND RESIDUES 150, 151 FROM MONOMER A, 54, 55, 288 AND 289 FROM MONOMER C WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5, 45-53, 290-292 FROM ALL THREE NCS MONOMERS AND RESIDUES 150, 151 FROM MONOMER A, 54, 55, 288 AND 289 FROM MONOMER C WERE DISORDERED AND WERE OMITTED FROM THE MODEL.
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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: 39.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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