+
Open data
-
Basic information
Entry | Database: PDB / ID: 1edm | ||||||
---|---|---|---|---|---|---|---|
Title | EPIDERMAL GROWTH FACTOR-LIKE DOMAIN FROM HUMAN FACTOR IX | ||||||
![]() | FACTOR IX | ||||||
![]() | COAGULATION FACTOR / EPIDERMAL GROWTH FACTOR / EGF / CALCIUM-BINDING / EGF-LIKE DOMAIN / STRUCTURE AND FUNCTION / HUMAN FACTOR IX | ||||||
Function / homology | ![]() Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation ...Defective F9 secretion / Defective gamma-carboxylation of F9 / coagulation factor IXa / Defective F9 activation / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / zymogen activation / Extrinsic Pathway of Fibrin Clot Formation / Protein hydroxylation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Golgi lumen / blood coagulation / collagen-containing extracellular matrix / endopeptidase activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rao, Z. / Handford, P. / Mayhew, M. / Knott, V. / Brownlee, G.G. / Stuart, D. | ||||||
![]() | ![]() Title: The structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein-protein interactions. Authors: Rao, Z. / Handford, P. / Mayhew, M. / Knott, V. / Brownlee, G.G. / Stuart, D. #1: ![]() Title: Crystallization of a Calcium-Binding Egf-Like Domain Authors: Rao, Z. / Handford, P. / Mayhew, M. / Knott, V. / Brownlee, G.G. / Stuart, D. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 31.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 21.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 370.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 374.2 KB | Display | |
Data in XML | ![]() | 3.6 KB | Display | |
Data in CIF | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein/peptide | Mass: 4279.635 Da / Num. of mol.: 2 / Fragment: EPIDERMAL GROWTH FACTOR-LIKE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 30 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.3 / Details: pH 7.3 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 289 K / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: SIEMENS / Detector: IMAGE PLATE / Date: Jan 1, 1992 |
Radiation | Monochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→30 Å / Num. obs: 1196 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.5→1.65 Å / % possible all: 92 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. obs: 13041 / % possible obs: 94.5 % / Redundancy: 3.7 % / Num. measured all: 48451 / Rmerge(I) obs: 0.102 |
Reflection shell | *PLUS % possible obs: 92 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: NMR MODEL Resolution: 1.5→30 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |