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- PDB-5jba: Crystal structure of factor IXa variant V16I K98T Y177T I212V in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jba | ||||||
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Title | Crystal structure of factor IXa variant V16I K98T Y177T I212V in complex with PPACK | ||||||
![]() | (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 | ![]() | 193.5 KB | Display | ![]() |
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PDB format | ![]() | 155 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 749.3 KB | Display | ![]() |
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Full document | ![]() | 752 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jb8C ![]() 5jb9C ![]() 5jbbC ![]() 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 I212V Source method: isolated from a genetically manipulated source Details: Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 244 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/0G6.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0G6.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-0G6 / |
#5: Chemical | ChemComp-DMS / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.91 % |
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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, 18% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 30, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→54.37 Å / Num. obs: 54056 / % possible obs: 96.34 % / Redundancy: 4.7 % / Biso Wilson estimate: 19.04 Å2 / Rmerge(I) obs: 0.04709 / Net I/σ(I): 21.52 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.1471 / Mean I/σ(I) obs: 3.49 / % possible all: 90.52 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2wph Resolution: 1.4→54.37 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.77 / 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: 172.93 Å2 / Biso mean: 38.0092 Å2 / Biso min: 13.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→54.37 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: 18
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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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