[English] 日本語
![](img/lk-miru.gif)
- PDB-3p06: Crystal structure of Tellina virus 1 VP4 protease in the form of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3p06 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Tellina virus 1 VP4 protease in the form of an intra-molecular(cis)acyl-enzyme complex. | ||||||
![]() | VP4 protein | ||||||
![]() | HYDROLASE / cis-cleavage / intramolecular acyl-enzyme / ester-linkage / alpha/beta protein / protease / polyprotein processing / acyl-enzyme | ||||||
Function / homology | ![]() serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chung, I.Y.W. / Paetzel, M. | ||||||
![]() | ![]() Title: Crystal Structure of a Viral Protease Intramolecular Acyl-enzyme Complex: INSIGHTS INTO cis-CLEAVAGE AT THE VP4/VP3 JUNCTION OF TELLINA BIRNAVIRUS. Authors: Chung, I.Y. / Paetzel, M. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Expression, purification and crystallization of VP4 protease from Tellina virus 1. Authors: Chung, I.Y. / Paetzel, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 83.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 68.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 465 KB | Display | |
Data in XML | ![]() | 10.1 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 20563.883 Da / Num. of mol.: 1 / Fragment: UNP residues 637-830 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 6 types, 54 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BME.gif)
![](data/chem/img/URE.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-BME / | #5: Chemical | ChemComp-URE / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.86 % |
---|---|
Crystal grow | Temperature: 296 K / pH: 5 Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 ...Details: reservoir: 21% PEG8000, 0.55M ammonium sulfate. drop: On a coverslip, 1 microliter of VP4 was mixed with 1 microliter of reservoir reagent(21% PEG8000, 0.55M ammonium sulfate) and 1 microliter of 0.2M urea as additive. To aid in crystal nucleation, this drop was seeded with 1 microliter of selenomethionine- labelled crystal from an older drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 28, 2010 Details: DCM WITH CRYO-COOLED 1ST CRYSTAL SAGITTALLY BENT 2ND CRYSTAL FOLLOWED BY VERTICALLY FOCUSING MIRROR. |
Radiation | Monochromator: A DOUBLE CRYSTAL MONOCHROMATOR (DCM) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97893 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52 Å / Num. obs: 13466 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.3 / % possible all: 98.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 28.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→52 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|