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- PDB-8cdm: Plasmodium falciparum Myosin A full-length, post-rigor state comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cdm | ||||||
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Title | Plasmodium falciparum Myosin A full-length, post-rigor state complexed to the inhibitor KNX-002 | ||||||
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![]() | MOTOR PROTEIN / Malaria / Plasmodium falciparum / Myosin A / KNX-002 / antimalarial treatment / molecular motors | ||||||
Function / homology | ![]() pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity ...pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.E. / Mueller-Dieckmann, C. / Baum, J. / Trybus, K.M. / Houdusse, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Plasmodium falciparum Myosin A full-length, post-rigor state complexed to the inhibitor KNX-002 Authors: Moussaoui, D. / Robblee, J.P. / Robert-Paganin, J. / Auguin, D. / Fisher, F. / Fagnant, P.M. / MacFarlane, J.E. / Schaletzky, J. / Wehri, E. / Mueller-Dieckmann, C. / Baum, J. / Trybus, K.M. / Houdusse, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 538.8 KB | Display | ![]() |
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PDB format | ![]() | 365.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 789.5 KB | Display | ![]() |
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Full document | ![]() | 803.5 KB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 59.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ycyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 3 types, 3 molecules ABE
#1: Protein | Mass: 92474.305 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: MyoA, PF13_0233, PF3D7_1342600 / Production host: ![]() ![]() |
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#2: Protein | Mass: 23510.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: PF3D7_1246400 / Production host: ![]() ![]() |
#3: Protein | Mass: 15692.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: CK202_4702 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 360 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/KQ0.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/KQ0.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-KQ0 / | #6: Chemical | ChemComp-PG4 / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.79 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 2.0 M ammonium sulfate, 0.1M sodium HEPES pH 7,5, 4% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→94.97 Å / Num. obs: 55344 / % possible obs: 93.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 55.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.35→2.53 Å / Rmerge(I) obs: 1.672 / Num. unique obs: 2767 / CC1/2: 0.578 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YCY Resolution: 2.35→46.44 Å / SU ML: 0.2676 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1792 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 58.72 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→46.44 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.97217217614 Å / Origin y: 0.433284134512 Å / Origin z: 37.62087237 Å
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Refinement TLS group | Selection details: all |