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Yorodumi- PDB-6i4d: Crystal Structure of Plasmodium falciparum actin I in the Mg-K-AT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i4d | ||||||||||||
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Title | Crystal Structure of Plasmodium falciparum actin I in the Mg-K-ATP/ADP state | ||||||||||||
Components |
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Keywords | CONTRACTILE PROTEIN / hydrolase / filamentous / glideosome / cytoskeleton | ||||||||||||
Function / homology | Function and homology information glial filament / plastid inheritance / schizogony / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy / regulation of establishment of T cell polarity ...glial filament / plastid inheritance / schizogony / apical ectoplasmic specialization / basal ectoplasmic specialization / Caspase-mediated cleavage of cytoskeletal proteins / symbiont-mediated actin polymerization-dependent cell-to-cell migration in host / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / actin cap / Neutrophil degranulation / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / entry into host cell by a symbiont-containing vacuole / actin filament severing / actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / barbed-end actin filament capping / cell projection assembly / cardiac muscle cell contraction / podosome / relaxation of cardiac muscle / positive regulation of p38MAPK cascade / phagocytosis, engulfment / positive regulation of cardiac muscle hypertrophy / hepatocyte apoptotic process / sarcoplasm / cilium assembly / cellular response to cadmium ion / vesicle-mediated transport / phagocytic vesicle / cytoskeleton organization / ruffle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / Neutrophil degranulation / central nervous system development / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / structural constituent of cytoskeleton / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / calcium ion binding / perinuclear region of cytoplasm / ATP hydrolysis activity / protein-containing complex / extracellular space / extracellular region / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å | ||||||||||||
Authors | Kumpula, E.-P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I. | ||||||||||||
Funding support | Finland, Norway, 3items
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Citation | Journal: Plos Biol. / Year: 2019 Title: Atomic view into Plasmodium actin polymerization, ATP hydrolysis, and fragmentation. Authors: Kumpula, E.P. / Lopez, A.J. / Tajedin, L. / Han, H. / Kursula, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i4d.cif.gz | 443.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i4d.ent.gz | 305.7 KB | Display | PDB format |
PDBx/mmJSON format | 6i4d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i4d_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6i4d_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6i4d_validation.xml.gz | 29.4 KB | Display | |
Data in CIF | 6i4d_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4d ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4d | HTTPS FTP |
-Related structure data
Related structure data | 6i4eC 6i4fC 6i4gC 6i4hC 6i4iC 6i4jC 6i4kC 6i4lC 6i4mC 4cbuS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AG
#1: Protein | Mass: 42047.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8I4X0 |
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#2: Protein | Mass: 14239.979 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsn, Gsb / Production host: Escherichia coli (E. coli) / References: UniProt: P13020 |
-Non-polymers , 9 types, 699 molecules
#3: Chemical | ChemComp-ATP / | ||||||||
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#4: Chemical | ChemComp-ADP / | ||||||||
#5: Chemical | ChemComp-MG / | ||||||||
#6: Chemical | ChemComp-K / | ||||||||
#7: Chemical | #8: Chemical | ChemComp-BTB / | #9: Chemical | ChemComp-CL / | #10: Chemical | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 23%(w/v) PEG3350, 0.1 M BIS-TRIS pH 6.0, 0.2M K-SCN; 20% PEG400 used for cryoprotection |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.031 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.031 Å / Relative weight: 1 |
Reflection | Resolution: 1.24→59.93 Å / Num. obs: 152407 / % possible obs: 98.8 % / Redundancy: 7 % / Biso Wilson estimate: 12.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.24→1.28 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.071 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 13428 / CC1/2: 0.509 / Rpim(I) all: 0.5109 / Rrim(I) all: 1.193 / % possible all: 88.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CBU Resolution: 1.24→59.93 Å / SU ML: 0.1323 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 14.6308
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.24→59.93 Å
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Refine LS restraints |
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LS refinement shell |
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