[English] 日本語
Yorodumi- PDB-4mo3: Crystal Structure of Porcine C2 Domain of Blood Coagulation Facto... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mo3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Porcine C2 Domain of Blood Coagulation Factor VIII | ||||||
Components | Coagulation factor VIII | ||||||
Keywords | BLOOD CLOTTING / Blood coagulation domain | ||||||
Function / homology | Function and homology information blood coagulation, intrinsic pathway / acute-phase response / signaling receptor activity / oxidoreductase activity / copper ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.702 Å | ||||||
Authors | Spiegel, P.C. / Brison, C. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Porcine C2 Domain of Blood Coagulation Factor VIII (FoldIt Target) Authors: Spiegel, P.C. / Brison, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4mo3.cif.gz | 50 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4mo3.ent.gz | 34 KB | Display | PDB format |
PDBx/mmJSON format | 4mo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mo3_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4mo3_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 4mo3_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | 4mo3_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mo/4mo3 ftp://data.pdbj.org/pub/pdb/validation_reports/mo/4mo3 | HTTPS FTP |
-Related structure data
Related structure data | 1d7pS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19903.359 Da / Num. of mol.: 1 / Fragment: C2 domain (UNP residues 1971-2129) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: F8, CF8 / Production host: Escherichia coli (E. coli) / References: UniProt: P12263 |
---|---|
#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.36 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 10.4 Details: 2:1 crystallization buffer (0.1 M magnesium acetate, 10% ethanol) to protein, crystals formed overnight with 0.1 M CHES buffer and 220 uL Hampton Research Al's oil over 400 uL reservoir, pH ...Details: 2:1 crystallization buffer (0.1 M magnesium acetate, 10% ethanol) to protein, crystals formed overnight with 0.1 M CHES buffer and 220 uL Hampton Research Al's oil over 400 uL reservoir, pH 10.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 98 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 2, 2013 / Details: Confocal VarimaxHR |
Radiation | Monochromator: VarimaxHR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→31.912 Å / Num. all: 19595 / Num. obs: 19595 / % possible obs: 97.42 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8 |
Reflection shell | Highest resolution: 1.7 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D7P Resolution: 1.702→31.912 Å / SU ML: 0.15 / σ(F): 1.39 / Phase error: 19.77 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.702→31.912 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|