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Yorodumi- PDB-7qox: Factor XI and Plasma Kallikrein apple domain structures reveals d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qox | ||||||
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Title | Factor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes | ||||||
Components |
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Keywords | BLOOD CLOTTING / Plasma kallikrein (PK) / High molecular weight kininogen (HK) / Factor XII (FXII) / Factor XI (FXI) / Factor IX (FIX) / bradykinin (BK) | ||||||
Function / homology | Function and homology information plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / negative regulation of cell adhesion / negative regulation of blood coagulation / zymogen activation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Defective factor XII causes hereditary angioedema ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / negative regulation of cell adhesion / negative regulation of blood coagulation / zymogen activation / cysteine-type endopeptidase inhibitor activity / plasminogen activation / Defective factor XII causes hereditary angioedema / Activation of Matrix Metalloproteinases / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / platelet alpha granule lumen / negative regulation of proteolysis / Post-translational protein phosphorylation / hormone activity / vasodilation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / heparin binding / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / inflammatory response / positive regulation of apoptotic process / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å | ||||||
Authors | Li, C. / Awital, B. / Wong, S. / Dreveny, I. / Meijers, J. / Emsley, J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J Thromb Haemost / Year: 2019 Title: Plasma kallikrein structure reveals apple domain disc rotated conformation compared to factor XI. Authors: Li, C. / Voos, K.M. / Pathak, M. / Hall, G. / McCrae, K.R. / Dreveny, I. / Li, R. / Emsley, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qox.cif.gz | 173.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qox.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 7qox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/7qox ftp://data.pdbj.org/pub/pdb/validation_reports/qo/7qox | HTTPS FTP |
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-Related structure data
Related structure data | 6i44C 6i58SC 7qotC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABDC
#1: Protein | Mass: 41134.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KLKB1, KLK3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P03952 #2: Protein/peptide | Mass: 3263.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: KNG1, BDK, KNG / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01042 #7: Sugar | |
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-Non-polymers , 6 types, 346 molecules
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-PEG / #5: Chemical | #6: Chemical | #8: Chemical | ChemComp-PG6 / | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
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Crystal grow | Temperature: 288 K / Method: evaporation Details: Morpheus screen H9 condition: 0.1M amino acids, 0.1M buffer system 3 pH8.5, 30% precipitant mix 1. |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→29.64 Å / Num. obs: 38760 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.46 Å2 / CC1/2: 0.987 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.32→2.4 Å / Num. unique obs: 9002 / CC1/2: 0.597 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I58 Resolution: 2.32→29.64 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.15 / 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: 99.07 Å2 / Biso mean: 33.7441 Å2 / Biso min: 14.06 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.32→29.64 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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