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Yorodumi- PDB-4fhw: Crystal structures of the Cid1 poly (U) polymerase reveal the mec... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fhw | ||||||
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Title | Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity - MgGTP bound | ||||||
Components | Poly(A) RNA polymerase protein cid1 | ||||||
Keywords | TRANSFERASE / nucleotidyltransferase / poly(U) polymerase | ||||||
Function / homology | Function and homology information polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / : / magnesium ion binding / RNA binding ...polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / : / magnesium ion binding / RNA binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Lunde, B.M. / Magler, I. / Meinhart, A. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2012 Title: Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity. Authors: Lunde, B.M. / Magler, I. / Meinhart, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fhw.cif.gz | 147.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fhw.ent.gz | 114.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fhw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fhw_validation.pdf.gz | 779.8 KB | Display | wwPDB validaton report |
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Full document | 4fhw_full_validation.pdf.gz | 780.3 KB | Display | |
Data in XML | 4fhw_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4fhw_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/4fhw ftp://data.pdbj.org/pub/pdb/validation_reports/fh/4fhw | HTTPS FTP |
-Related structure data
Related structure data | 4fh3SC 4fh5C 4fhpC 4fhvC 4fhxC 4fhyC 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: 39956.754 Da / Num. of mol.: 1 / Fragment: UNP residues 33-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)RIL References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-GTP / |
#3: Chemical | ChemComp-MG / |
#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: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: 100 mM CHES, pH 9.5, 5-10% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2011 |
Radiation | Monochromator: double crystal sagitally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.2 Å / Num. all: 13553 / Num. obs: 13540 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.43 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FH3 Resolution: 2.5→48.17 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / SU B: 18.673 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.291 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 29.447 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→48.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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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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