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Yorodumi- PDB-5jbc: Crystal structure of factor IXa variant V16I K98T Y177T I213V in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jbc | ||||||
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Title | Crystal structure of factor IXa variant V16I K98T Y177T I213V in complex with PPACK | ||||||
Components | (Coagulation factor IX) x 2 | ||||||
Keywords | HYDROLASE / Crystal structure of factor IXa variant K98T in complex with EGR-chloromethylketone | ||||||
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: 1.9 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 | 5jbc.cif.gz | 181.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jbc.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jbc_validation.pdf.gz | 738.5 KB | Display | wwPDB validaton report |
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Full document | 5jbc_full_validation.pdf.gz | 740.9 KB | Display | |
Data in XML | 5jbc_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 5jbc_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jbc ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jbc | HTTPS FTP |
-Related structure data
Related structure data | 5jb8C 5jb9C 5jbaC 5jbbC 2wphS 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
#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: 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.) Homo sapiens (human) / Gene: F9 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): NiCo21 / References: UniProt: P00740, coagulation factor IXa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-0G6 / |
#5: 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: 2.18 Å3/Da / Density % sol: 43.69 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
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: 1.9→27.25 Å / Num. obs: 23122 / % possible obs: 100 % / Redundancy: 16.3 % / Biso Wilson estimate: 25.07 Å2 / Rmerge(I) obs: 0.1505 / Net I/σ(I): 12.35 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 15.2 % / Rmerge(I) obs: 0.8739 / Mean I/σ(I) obs: 3.14 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wph Resolution: 1.9→27.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.71 / 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: 224.86 Å2 / Biso mean: 45.21 Å2 / Biso min: 12.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→27.25 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: 8 / % reflection obs: 100 %
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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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