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Yorodumi- PDB-8cdm: Plasmodium falciparum Myosin A full-length, post-rigor state comp... -
+Open data
-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 | ||||||
Components |
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Keywords | MOTOR PROTEIN / Malaria / Plasmodium falciparum / Myosin A / KNX-002 / antimalarial treatment / molecular motors | ||||||
Function / homology | Function and homology information pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding ...pellicle / glideosome / inner membrane pellicle complex / vesicle transport along actin filament / myosin II complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | 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 | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cdm.cif.gz | 538.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cdm.ent.gz | 365.6 KB | Display | PDB format |
PDBx/mmJSON format | 8cdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/8cdm ftp://data.pdbj.org/pub/pdb/validation_reports/cd/8cdm | HTTPS FTP |
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-Related structure data
Related structure data | 6ycyS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: MyoA, PF13_0233, PF3D7_1342600 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8IDR3 |
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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.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PF3D7_1246400 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4W8 |
#3: Protein | Mass: 15692.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: CK202_4702 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BQX1 |
-Non-polymers , 4 types, 360 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1.0722 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |