[English] 日本語
![](img/lk-miru.gif)
- PDB-2dw2: Crystal structure of VAP2 from Crotalus atrox venom (Form 2-5 crystal) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2dw2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of VAP2 from Crotalus atrox venom (Form 2-5 crystal) | |||||||||
![]() | Catrocollastatin | |||||||||
![]() | APOPTOSIS / TOXIN / apoptotic toxin / SVMP / metalloproteinase | |||||||||
Function / homology | ![]() Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Takeda, S. / Igarashi, T. / Araki, S. | |||||||||
![]() | ![]() Title: Crystal structures of catrocollastatin/VAP2B reveal a dynamic, modular architecture of ADAM/adamalysin/reprolysin family proteins Authors: Igarashi, T. / Araki, S. / Mori, H. / Takeda, S. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 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. #2: ![]() 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. #3: Journal: ENDOTHELIUM / Year: 2007 Title: cDNA cloning and some additional peptide characterization of a single-chain vascular apoptosis-inducing protein, VAP2 Authors: Masuda, S. / Maeda, H. / Miao, J.Y. / Hayashi, H. / Araki, S. #4: Journal: Eur.J.Biochem. / Year: 1998 Title: Two vascular apoptosis-inducing proteins from snake venom are members of the metalloprotease/disintegrin family Authors: Masuda, S. / Hayashi, H. / Araki, S. | |||||||||
History |
| |||||||||
Remark 999 | SEQUENCE There is difference between the SEQRES and the sequence database. The depositors believe ...SEQUENCE There is difference between the SEQRES and the sequence database. The depositors believe it is a variant. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 182.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 144.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 34.2 KB | Display | |
Data in CIF | ![]() | 47.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dw0C ![]() 2dw1C ![]() 2eroS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 46912.762 Da / Num. of mol.: 2 / Fragment: residues 191-609 / Source method: isolated from a natural source Source: (natural) ![]() References: UniProt: Q90282 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.13 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 4% n-propanol, 16.2% PEG8000, 0.18M calcium acetate, 0.09M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2005 |
Radiation | Monochromator: rotated-inclined double-crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 28047 / Num. obs: 26911 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2313 / % possible all: 82.5 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2ERO Resolution: 2.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.8 Å
|