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- PDB-4fhy: Crystal structures of the Cid1 poly (U) polymerase reveal the mec... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fhy | ||||||
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Title | Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity - Mg 3'-dATP bound | ||||||
![]() | Poly(A) RNA polymerase protein cid1 | ||||||
![]() | TRANSFERASE / nucleotidyltransferase / poly(U) polymerase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lunde, B.M. / Magler, I. / Meinhart, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144 KB | Display | ![]() |
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PDB format | ![]() | 111.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.9 KB | Display | ![]() |
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Full document | ![]() | 764 KB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fh3SC ![]() 4fh5C ![]() 4fhpC ![]() 4fhvC ![]() 4fhwC ![]() 4fhxC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 39956.754 Da / Num. of mol.: 1 / Fragment: UNP residues 33-377 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-3AT / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.33 % |
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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: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2011 |
Radiation | Monochromator: double crystal sagitally focusing Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9718 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.6 Å / Num. all: 10779 / Num. obs: 10732 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Net I/σ(I): 11.28 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 2.28 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FH3 Resolution: 2.7→41.56 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.881 / SU B: 30.661 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.378 / 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: 29.499 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→41.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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