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- PDB-5jbb: Crystal structure of factor IXa variant V16I K98T Y177T I213V in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jbb | ||||||
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Title | Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with EGR-chloromethylketone | ||||||
![]() | (Coagulation factor ...) x 2 | ||||||
![]() | HYDROLASE / BLOOD CLOTTING / GLYCOPROTEIN / HAEMOSTASIS | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kristensen, L.H. / Brandstetter, H. | ||||||
![]() | ![]() Title: Releasing the brakes in coagulation Factor IXa by co-operative maturation of the substrate-binding site. Authors: Kristensen, L.H. / Olsen, O.H. / Blouse, G.E. / Brandstetter, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 185 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 801.6 KB | Display | ![]() |
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Full document | ![]() | 804.2 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jb8C ![]() 5jb9C ![]() 5jbaC ![]() 5jbcC ![]() 2wphS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Coagulation factor ... , 2 types, 2 molecules ES
#1: Protein | Mass: 6395.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fragment: EGF2 DOMAIN, RESIDUES 133-191 / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 26100.672 Da / Num. of mol.: 1 / Mutation: V16I K98T Y177T I213V Source method: isolated from a genetically manipulated source Details: Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 272 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/0GJ.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0GJ.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-0GJ / |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 6 mg/mL protein-inhibitor complex, 0.1M MES pH 6.5, 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 29, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→21.6 Å / Num. obs: 41579 / % possible obs: 99.73 % / Redundancy: 6 % / Biso Wilson estimate: 20.48 Å2 / Rmerge(I) obs: 0.0698 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.56→1.616 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.7482 / Mean I/σ(I) obs: 2.1 / % possible all: 99.49 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2wph Resolution: 1.56→21.599 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.58 Å2 / Biso mean: 36.2923 Å2 / Biso min: 10.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.56→21.599 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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