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- PDB-6i58: Allosteric activation of human prekallikrein by apple domain disc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i58 | ||||||||||||
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Title | Allosteric activation of human prekallikrein by apple domain disc rotation | ||||||||||||
![]() | Coagulation factor XI | ||||||||||||
![]() | BLOOD CLOTTING / Prekallikrein / activation / high molecular weight kininogen / Factor XI | ||||||||||||
Function / homology | ![]() coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, C. / Pathak, M. / McCrae, K. / Dreveny, I. / Emsley, J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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. #1: Journal: Nat. Struct. Mol. Biol. / Year: 2006 Title: Crystal structure of the factor XI zymogen reveals a pathway for transactivation. Authors: Papagrigoriou, E. / McEwan, P.A. / Walsh, P.N. / Emsley, J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.3 KB | Display | ![]() |
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PDB format | ![]() | 102.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 846.4 KB | Display | ![]() |
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Full document | ![]() | 856.7 KB | Display | |
Data in XML | ![]() | 24 KB | Display | |
Data in CIF | ![]() | 33 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6i44C ![]() 7qotC ![]() 7qoxC ![]() 2f83 ![]() 6i4w C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 68116.609 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Sugars , 2 types, 3 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 3 types, 89 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.07 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 0.1 M SODIUM HEPES AND 22% (V/V) PEG 1000, PH 7.5, EVAPORATION, TEMPERATURE 293K PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 5, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.87 Å / Num. obs: 23616 / % possible obs: 99.3 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.0875 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2F83 ![]() 2f83 Resolution: 2.6→37.71 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.9 / SU B: 12.797 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R: 0.57 / ESU R Free: 0.34 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→37.71 Å
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Refine LS restraints |
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