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Open data
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Basic information
Entry | Database: PDB / ID: 4nku | ||||||
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Title | Structure of Cid1 in complex with its short product ApU | ||||||
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![]() | TRANSFERASE/RNA / poly(U) polymerase / nucleotidyl tranfer domain / PAP-associated domain / UTP binding / TRANSFERASE-RNA complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Munoz-Tello, P. / Gabus, C. / Thore, S. | ||||||
![]() | ![]() Title: A critical switch in the enzymatic properties of the Cid1 protein deciphered from its product-bound crystal structure. Authors: Munoz-Tello, P. / Gabus, C. / Thore, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.5 KB | Display | ![]() |
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PDB format | ![]() | 116.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 463.8 KB | Display | ![]() |
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Full document | ![]() | 470.8 KB | Display | |
Data in XML | ![]() | 27.5 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nktC ![]() 4ep7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 38984.703 Da / Num. of mol.: 2 / Fragment: UNP residues 40-377 / Mutation: D160A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cid1, SPAC19D5.03 / Plasmid: pET42-based / Production host: ![]() ![]() References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: RNA chain | Mass: 590.414 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1 M imidazole/MES, pH 6.1, 20% glycerol, 10% PEG4000, 126 mM halogens (sodium iodide, sodium bromide, sodium fluoride), 10 mM TCEP, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2012 |
Radiation | Monochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9394 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→45.337 Å / Num. all: 49786 / Num. obs: 49569 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.14 |
Reflection shell | Highest resolution: 1.94 Å / Redundancy: 5 % / Rmerge(I) obs: 0.086 / Mean I/σ(I) obs: 2.28 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4EP7 Resolution: 1.94→45.337 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 22.77 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.94→45.337 Å
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Refine LS restraints |
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LS refinement shell |
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