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- PDB-6i44: 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: 6i44 | ||||||||||||
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Title | Allosteric activation of human prekallikrein by apple domain disc rotation | ||||||||||||
![]() | Plasma kallikrein![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Li, C. / Pathak, M. / MaCrae, 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 | ![]() | 161.2 KB | Display | ![]() |
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PDB format | ![]() | 120.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i58C ![]() 7qotC ![]() 7qoxC ![]() 2f83 S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | ![]() Mass: 70152.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#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 |
-Non-polymers , 13 types, 665 molecules ![](data/chem/img/BEN.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/SER.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BEN / ![]() | ||||||||||||
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#4: Chemical | ChemComp-MPD / (![]() | ||||||||||||
#5: Chemical | ChemComp-PE4 / ![]() | ||||||||||||
#6: Chemical | ChemComp-SO4 / ![]() | ||||||||||||
#7: Chemical | ChemComp-CL / ![]() | ||||||||||||
#8: Chemical | ChemComp-NA / | ||||||||||||
#9: Chemical | ![]() #10: Chemical | ChemComp-GOL / ![]() #11: Chemical | ChemComp-FMT / ![]() #12: Chemical | ChemComp-ACT / ![]() #13: Chemical | ChemComp-GLY / | ![]() #14: Chemical | ChemComp-SER / | ![]() #15: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.5 % |
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Crystal grow![]() | Temperature: 293 K / Method: evaporation / pH: 7.5 Details: 0.1M carboxylic acid, 0.1M Hepes/mops pH 7.5, 12.5%MPD, 12.5%PEG1000, 12.5%PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.36→129.63 Å / Num. obs: 141376 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.999 / Net I/σ(I): 0.05 |
Reflection shell | Resolution: 1.36→6.08 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.682 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 10225 / CC1/2: 0.76 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2F83 ![]() 2f83 Resolution: 1.36→28.05 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.958 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.056 / 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: 18.539 Å2
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Refinement step | Cycle: 1 / Resolution: 1.36→28.05 Å
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Refine LS restraints |
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