+Open data
-Basic information
Entry | Database: PDB / ID: 6ycz | ||||||
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Title | Plasmodium falciparum Myosin A delta-Nter, Post-Rigor state | ||||||
Components |
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Keywords | MOTOR PROTEIN / Myosin A / Myosin / Plasmodium / Myosin XIV / Myosin 14 | ||||||
Function / homology | Function and homology information pellicle / glideosome / inner membrane pellicle complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding ...pellicle / glideosome / inner membrane pellicle complex / myosin complex / microfilament motor activity / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å | ||||||
Authors | Moussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.B. / Robert-Paganin, J. / Trybus, K.M. / Houdusse, A. | ||||||
Funding support | 1items
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Citation | Journal: Elife / Year: 2020 Title: Full-length Plasmodium falciparum myosin A and essential light chain PfELC structures provide new anti-malarial targets. Authors: Moussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.B. / Haase, S. / Blake, T.C.A. / Baum, J. / Robert-Paganin, J. / Trybus, K.M. / Houdusse, A. #1: Journal: To Be Published Title: Plasmodium Myosin A motor properties are tuned by multiple sequence and structural adaptations Authors: Moussaoui, D. / Robblee, J.P. / Auguin, D. / Krementsova, E.M. / Robert-Paganin, J. / Houdusse, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ycz.cif.gz | 438.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ycz.ent.gz | 358.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ycz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ycz_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6ycz_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6ycz_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 6ycz_validation.cif.gz | 50.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yc/6ycz ftp://data.pdbj.org/pub/pdb/validation_reports/yc/6ycz | HTTPS FTP |
-Related structure data
Related structure data | 6ycxC 6ycyC 6i7dS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 ABC
#1: Protein | Mass: 92394.320 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote) Strain: isolate 3D7 / Gene: PF13_0233 / 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 (isolate NF54) (eukaryote) Strain: isolate NF54 / Gene: CK202_1873, PFNF54_03975 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: W7K1J7 |
#3: Protein | Mass: 15692.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (isolate NF54) (eukaryote) Strain: isolate NF54 / Gene: CK202_4702 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A2I0BQX1 |
-Non-polymers , 5 types, 11 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-ADP / | #8: 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: 3.34 Å3/Da / Density % sol: 63.21 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 2.0M Ammonium sulfate, 0.1M Sodium HEPES pH 7.5, 6% PEG400 |
-Data collection
Diffraction | Mean temperature: 77.36 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 3.27→48.3 Å / Num. obs: 27977 / % possible obs: 99.88 % / Redundancy: 12.8 % / CC1/2: 0.992 / Net I/σ(I): 9.02 |
Reflection shell | Resolution: 3.27→3.387 Å / Num. unique obs: 2748 / CC1/2: 0.553 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6I7D Resolution: 3.27→48.3 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.884 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.4
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Displacement parameters | Biso max: 196.83 Å2 / Biso mean: 92.68 Å2 / Biso min: 32.25 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.27→48.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.27→3.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
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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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