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- PDB-8eph: Crystal structure of human coagulation factor IXa (S195A), apo-fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eph | ||||||
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Title | Crystal structure of human coagulation factor IXa (S195A), apo-form, DES-GLA | ||||||
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![]() | BLOOD CLOTTING / coagulation factor IX / apo form / hydrolase | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Kolyadko, V.N. / Krishnaswamy, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Allosteric Control of Coagulation Factor IXa via Its Exosite II Regulates Blood Clotting Authors: Kolyadko, V.N. / Layzer, J.M. / Perry, K. / Sullenger, B.A. / Krishnaswamy, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 154.3 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
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Full document | ![]() | 472.6 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 42.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8epcC ![]() 8epkC ![]() 5jb9S ![]() 5vygS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11316.673 Da / Num. of mol.: 2 / Fragment: furin cleavage site (RRKR) inserted Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 26174.818 Da / Num. of mol.: 2 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Sugar | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M Na Citrate pH 5.0; 30% Jeffamine ED-2001 pH 7.0 PH range: 5.0 - 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.88→78.16 Å / Num. obs: 52703 / % possible obs: 99.3 % / Redundancy: 6 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Net I/σ(I): 11.1 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 4
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JB9, 5VYG Resolution: 1.88→78.16 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.474 / SU ML: 0.099 / SU R Cruickshank DPI: 0.1583 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.46 Å2 / Biso mean: 30.374 Å2 / Biso min: 15.09 Å2
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Refinement step | Cycle: final / Resolution: 1.88→78.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.928 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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