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Yorodumi- PDB-6i4m: Crystal Structure of Plasmodium berghei actin II in the Mg-ADP state -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i4m | ||||||||||||
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Title | Crystal Structure of Plasmodium berghei actin II in the Mg-ADP state | ||||||||||||
Components |
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Keywords | CONTRACTILE PROTEIN / hydrolase / filamentous / cytoskeleton | ||||||||||||
Function / homology | Function and homology information positive regulation of development of symbiont in host / exit from host cell / glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization ...positive regulation of development of symbiont in host / exit from host cell / glial filament / apical ectoplasmic specialization / basal ectoplasmic specialization / male gamete generation / Caspase-mediated cleavage of cytoskeletal proteins / 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 / cilium organization / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / 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 / ruffle / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / Neutrophil degranulation / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / myelin sheath / actin binding / actin cytoskeleton organization / amyloid fibril formation / cytoskeleton / 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 berghei (eukaryote) Mus musculus (house mouse) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.873 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 | 6i4m.cif.gz | 371.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i4m.ent.gz | 252.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i4m_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6i4m_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6i4m_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 6i4m_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i4/6i4m ftp://data.pdbj.org/pub/pdb/validation_reports/i4/6i4m | HTTPS FTP |
-Related structure data
Related structure data | 6i4dC 6i4eC 6i4fC 6i4gC 6i4hC 6i4iC 6i4jC 6i4kC 6i4lC 4cbxS C: citing same article (ref.) S: Starting model for refinement |
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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 , 2 types, 2 molecules AG
#1: Protein | Mass: 42869.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium berghei (strain Anka) (eukaryote) Strain: Anka / Gene: PB001050.02.0 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4YU79 |
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#2: Protein | Mass: 14125.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: N-terminal GP results from cleavage with 3C protease Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsn, Gsb / Production host: Escherichia coli (E. coli) / References: UniProt: P13020 |
-Non-polymers , 5 types, 450 molecules
#3: Chemical | ChemComp-ADP / | ||||
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#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | #6: Chemical | #7: 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: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 23% PEG3350, 0.1M BIS-TRIS pH 6.3, 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: 1.873→64.88 Å / Num. obs: 73248 / % possible obs: 93.81 % / Redundancy: 1.9 % / Biso Wilson estimate: 22.46 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.03798 / Rpim(I) all: 0.03352 / Rrim(I) all: 0.05083 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.873→1.94 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.2955 / Num. unique obs: 4975 / CC1/2: 0.826 / Rpim(I) all: 0.2727 / Rrim(I) all: 0.4032 / % possible all: 63.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CBX Resolution: 1.873→64.88 Å / SU ML: 0.1579 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 17.1608
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.873→64.88 Å
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Refine LS restraints |
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LS refinement shell |
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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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