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Open data
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Basic information
Entry | Database: PDB / ID: 6sny | |||||||||
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Title | Synthetic mimic of an EPCR-binding PfEMP1 bound to EPCR | |||||||||
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![]() | IMMUNE SYSTEM / PfEMP1 EPCR vaccine immunogen | |||||||||
Function / homology | ![]() negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space ...negative regulation of coagulation / Common Pathway of Fibrin Clot Formation / Cell surface interactions at the vascular wall / blood coagulation / signaling receptor activity / focal adhesion / centrosome / perinuclear region of cytoplasm / cell surface / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | synthetic construct (others)![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Barber, N.M. / Higgins, M.K. | |||||||||
Funding support | 1items
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![]() | ![]() Title: Structure-Guided Design of a Synthetic Mimic of an Endothelial Protein C Receptor-Binding PfEMP1 Protein. Authors: Barber, N.M. / Lau, C.K.Y. / Turner, L. / Watson, G. / Thrane, S. / Lusingu, J.P.A. / Lavstsen, T. / Higgins, M.K. #1: ![]() Title: Structure-guided design of a synthetic mimic of an EPCR-binding PfEMP1 protein Authors: Barber, N.M. / Lau, C.K.Y. / Turner, L. / Watson, G. / Thrane, S. / Luisnghu, J.P.A. / Lavstsen, T. / Higgins, M.K. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 213.2 KB | Display | ![]() |
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PDB format | ![]() | 181.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 836.1 KB | Display | ![]() |
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Full document | ![]() | 851.7 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 3 molecules ABC
#1: Protein | Mass: 15491.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() |
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#2: Protein | Mass: 22046.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Sugars , 3 types, 7 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #6: Sugar | |
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-Non-polymers , 1 types, 2 molecules ![](data/chem/img/PTY.gif)
#5: Chemical |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.87 Å3/Da / Density % sol: 79.05 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2M sodium citrate, 0.1M HEPES pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.11→46.88 Å / Num. obs: 20508 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 1 / Rrim(I) all: 0.079 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 3.11→3.19 Å / Num. unique obs: 1635 / CC1/2: 0.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso max: 260.27 Å2 / Biso mean: 128.47 Å2 / Biso min: 67.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.44 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.11→46.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.11→3.14 Å / Total num. of bins used: 50
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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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