[English] 日本語
![](img/lk-miru.gif)
- PDB-4fhv: Crystal structures of the Cid1 poly (U) polymerase reveal the mec... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4fhv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structures of the Cid1 poly (U) polymerase reveal the mechanism for UTP selectivity - MgCTP 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 151.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 118.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 791.3 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4fh3SC ![]() 4fh5C ![]() 4fhpC ![]() 4fhwC ![]() 4fhxC ![]() 4fhyC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
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 |
---|---|
#2: Chemical | ChemComp-CTP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.75 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 2.1→41.739 Å / Num. all: 22692 / Num. obs: 22623 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 6.9 / % possible all: 99.3 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4FH3 Resolution: 2.1→41.739 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.155 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 18.833 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.739 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|