[English] 日本語
![](img/lk-miru.gif)
- PDB-1uvk: The structural basis for RNA specificity and Ca2 inhibition of an... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1uvk | ||||||
---|---|---|---|---|---|---|---|
Title | The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex | ||||||
![]() | RNA-directed RNA polymerase | ||||||
![]() | TRANSFERASE / POLYMERASE-COMPLEX / OLIGONUCLEOTIDE / POLYMERASE | ||||||
Function / homology | ![]() RNA uridylyltransferase activity / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / DNA-templated transcription / RNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Salgado, P.S. / Makeyev, E.V. / Butcher, S. / Bamford, D. / Stuart, D.I. / Grimes, J.M. | ||||||
![]() | ![]() Title: The structural basis for RNA specificity and Ca2+ inhibition of an RNA-dependent RNA polymerase. Authors: Salgado, P.S. / Makeyev, E.V. / Butcher, S.J. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 405 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 329.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.5 MB | Display | |
Data in XML | ![]() | 75.8 KB | Display | |
Data in CIF | ![]() | 102.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1uviC ![]() 1uvjC ![]() 1uvlC ![]() 1uvmC ![]() 1uvnC ![]() 1hhsS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||
2 | ![]()
| ||||||||||||||||
3 | ![]()
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
| ||||||||||||||||
Details | THE POLYMERASE IS A MONOMER IN SOLUTION, BUT SINCE IT IS IN COMPLEX WITH RNA IN THIS ENTRY, THE OLIGOMER IS ANNOTATED AS A DIMER |
-
Components
-Protein , 1 types, 3 molecules ACE
#1: Protein | Mass: 74903.203 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 279 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/G.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/POP.gif)
![](data/chem/img/G.gif)
![](data/chem/img/GTP.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Compound details | FUNCTION: P2 IS ONE OF THE 4 STRUCTURAL PROTEINS OF THE POLYHEDRAL PROCAPSID, WHICH IS RESPONSIBLE ...FUNCTION: P2 IS ONE OF THE 4 STRUCTURAL |
---|---|
Sequence details | THE PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA SEQUENCE 5-U-U-U-C-C-3. HOWEVER, NO TRACE OF RNA WAS ...THE PROTEIN WAS CO-CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.3 Details: 100MM HEPES PH7.3, 13% PEG 20000, 2MM MNCL2, 2% EG, 0.036MG PROTEIN INCUBATED WITH 0.006MM 5NT RNA SOAKING: 25MM MGCL2, 40-60MM GTP, pH 7.30 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 6.7 / Method: vapor diffusion, sitting dropDetails: Butcher, S.J., (2000) Acta Crystallogr.,Sect.D, D56, 1473. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 150 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. obs: 97099 / % possible obs: 97.7 % / Observed criterion σ(I): 3.3 / Redundancy: 48 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.4 / % possible all: 96.1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. obs: 97851 / Num. measured all: 4701397 / Rmerge(I) obs: 0.136 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 96 % / Mean I/σ(I) obs: 3.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HHS Resolution: 2.45→19.98 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2002882.3 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DISORDERED LOOP: R607-E613. PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA OLIGO AND SOAKED WITH GTP. CATALYSIS OCCURED IN THE CRYSTAL AND THE GTP HYDROLYSIS PRODUCT ...Details: BULK SOLVENT MODEL USED DISORDERED LOOP: R607-E613. PROTEIN WAS CO-CRYSTALLIZED WITH A 5NT RNA OLIGO AND SOAKED WITH GTP. CATALYSIS OCCURED IN THE CRYSTAL AND THE GTP HYDROLYSIS PRODUCT GUANYLYL(3'-5') -GUANOSINE-5'- TRIPHOSPHATE (GPGPPP) AND THE BYPRODUCT PPI WERE DETECTED IN ED MAPS. NO RNA WAS TRACEABLE. S SITE 3'CYT RECOGNITION POCKET: LOOP: Y630-K631-W632 SUBSTRATE/BYPRODUCTS PORE: R225, R268,R270
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 32 Å2 / ksol: 0.343709 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→19.98 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.6 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|