[English] 日本語
![](img/lk-miru.gif)
- PDB-1iod: CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1iod | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE COAGULATION FACTOR X BINDING PROTEIN FROM SNAKE VENOM AND THE GLA DOMAIN OF FACTOR X | ||||||
![]() |
| ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / calcium bridging / domain swapping / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | ![]() coagulation factor Xa / positive regulation of leukocyte chemotaxis / blood coagulation / signaling receptor activity / toxin activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T. | ||||||
![]() | ![]() Title: Crystal structure of an anticoagulant protein in complex with the Gla domain of factor X. Authors: Mizuno, H. / Fujimoto, Z. / Atoda, H. / Morita, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 83.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 22.5 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 on special symmetry positions |
|
-
Components
#1: Protein | Mass: 14682.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
---|---|---|---|
#2: Protein | Mass: 14580.163 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() | ||
#3: Protein/peptide | Mass: 5734.670 Da / Num. of mol.: 1 / Fragment: GLA DOMAIN(RESIDUES 41-84) / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
#4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.73 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.9 Details: PEG8000, calcium chloride, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 11, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→100 Å / Num. all: 109232 / Num. obs: 20411 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.3→2.44 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.33 / Num. unique all: 3048 / % possible all: 90.3 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. measured all: 109232 |
Reflection shell | *PLUS Highest resolution: 2.3 Å / % possible obs: 92.5 % / Num. unique obs: 3206 / Rmerge(I) obs: 0.33 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY Resolution: 2.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018
| ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 2 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.3 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.5 | ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.301 / Rfactor Rwork: 0.302 |