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Yorodumi- PDB-5jb8: Crystal structure of factor IXa variant K98T in complex with EGR-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jb8 | ||||||
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Title | Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone | ||||||
Components | (Coagulation factor ...) x 2 | ||||||
Keywords | HYDROLASE / BLOOD CLOTTING / GLYCOPROTEIN / HAEMOSTASIS | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å | ||||||
Authors | Kristensen, L.H. / Brandstetter, H. | ||||||
Citation | Journal: Biochem.J. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jb8.cif.gz | 190.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jb8.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jb8_validation.pdf.gz | 784.8 KB | Display | wwPDB validaton report |
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Full document | 5jb8_full_validation.pdf.gz | 786.7 KB | Display | |
Data in XML | 5jb8_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 5jb8_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jb8 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jb8 | HTTPS FTP |
-Related structure data
Related structure data | 5jb9C 5jbaC 5jbbC 5jbcC 1wph S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): NiCo21 / References: UniProt: P00740, coagulation factor IXa |
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#2: Protein | Mass: 26162.742 Da / Num. of mol.: 1 / Mutation: K98T Source method: isolated from a genetically manipulated source Details: Fragment: CATALYTIC DOMAIN, RESIDUES 227-461 / Source: (gene. exp.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Nico21 / References: UniProt: P00740, coagulation factor IXa |
-Non-polymers , 4 types, 257 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.29 % |
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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, 18-20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 7, 2015 |
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: 1.45→16.77 Å / Num. all: 228593 / Num. obs: 51455 / % possible obs: 99.15 % / Redundancy: 4.4 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.08072 / Net I/σ(I): 7.22 |
Reflection shell | Resolution: 1.45→1.502 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.7014 / Mean I/σ(I) obs: 1.8 / % possible all: 98.97 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1wph 1wph Resolution: 1.45→16.77 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.05
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 144.3 Å2 / Biso mean: 32.3 Å2 / Biso min: 12.23 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→16.77 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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