[English] 日本語
![](img/lk-miru.gif)
- PDB-2ero: Crystal structure of vascular apoptosis-inducing protein-1(orthor... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ero | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form) | |||||||||
![]() | vascular apoptosis-inducing protein 1 | |||||||||
![]() | TOXIN / metalloprotease / disintegrin / calcium-binding / ADAM / SVMP / MDC protein | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / apoptotic process / protein homodimerization activity / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Takeda, S. / Igarashi, T. / Araki, S. | |||||||||
![]() | ![]() Title: Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold Authors: Takeda, S. / Igarashi, T. / Mori, H. / Araki, S. #1: ![]() Title: Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom Authors: Igarashi, T. / Oishi, Y. / Araki, S. / Mori, H. / Takeda, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 143.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 47.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2erpC ![]() 2erqC ![]() 1quaS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Details | Asymmetric unit contains one disulfide-linked homodimer molecule that is the biological unit. |
-
Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 47378.000 Da / Num. of mol.: 2 / Fragment: residues 184-610 / Source method: isolated from a natural source Source: (natural) ![]() Secretion: venom / References: GenBank: 11320556, UniProt: Q9DGB9*PLUS #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 210 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/3CO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/3CO.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-3CO / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15% PEG, 100mM sodium/cacodylate, 20mM cobaltous chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 15, 2004 |
Radiation | Monochromator: double diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 39161 / Num. obs: 38926 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3800 / % possible all: 98.8 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QUA Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.59 Å
|