[English] 日本語
![](img/lk-miru.gif)
- PDB-3gqh: Crystal Structure of the Bacteriophage phi29 gene product 12 C-te... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3gqh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment | ||||||
![]() | Preneck appendage protein | ||||||
![]() | VIRAL PROTEIN / beta barrel | ||||||
Function / homology | ![]() virus tail, fiber / symbiont entry into host cell via disruption of host cell envelope / adhesion receptor-mediated virion attachment to host cell / virion attachment to host cell / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xiang, Y. / Rossmann, M.G. | ||||||
![]() | ![]() Title: Crystallographic insights into the autocatalytic assembly mechanism of a bacteriophage tail spike. Authors: Xiang, Y. / Leiman, P.G. / Li, L. / Grimes, S. / Anderson, D.L. / Rossmann, M.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 108 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 452.6 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 29.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gq7C ![]() 3gq8C ![]() 3gq9C ![]() 3gqaC ![]() 3gqkC ![]() 3sucC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18014.301 Da / Num. of mol.: 3 / Fragment: D4, Residues 692-854 Source method: isolated from a genetically manipulated source Details: RESIDUES 692-854 EXPRESSED WITH A N-TERMIINAL HIS6 TAG Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Sequence details | THESE MUTATIONS MIGHT BE AN ACCUMULATE | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100mM Bis-Tris at pH 7.0, 20% PEG4K and 10% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 21, 2008 |
Radiation | Monochromator: SI(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→42.08 Å / Num. obs: 55084 / % possible obs: 99.5 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 1.8→1.86 Å / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 7 / Num. unique all: 5419 / Rsym value: 0.438 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.66 Å2 / Biso mean: 26.743 Å2 / Biso min: 8.85 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
|