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Yorodumi- PDB-5mvv: Crystal structure of Plasmodium falciparum actin I- gelsolin segm... -
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-Basic information
Entry | Database: PDB / ID: 5mvv | |||||||||
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Title | Crystal structure of Plasmodium falciparum actin I- gelsolin segment 1 -CdATP complex | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / experimental phasing / cadmium / atp / actin / SAD phasing | |||||||||
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 / SAD / Resolution: 1.4 Å | |||||||||
Authors | Panneerselvam, S. / Kumpula, E.-P. / Kursula, I. / Burkhardt, A. / Meents, A. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: Rapid cadmium SAD phasing at the standard wavelength (1 angstrom ). Authors: Panneerselvam, S. / Kumpula, E.P. / Kursula, I. / Burkhardt, A. / Meents, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mvv.cif.gz | 248.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mvv.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 5mvv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mvv_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5mvv_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5mvv_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 5mvv_validation.cif.gz | 38.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mv/5mvv ftp://data.pdbj.org/pub/pdb/validation_reports/mv/5mvv | HTTPS FTP |
-Related 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: 42047.676 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: PFL2215w / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf21 / References: UniProt: Q8I4X0 |
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#2: Protein | Mass: 14211.929 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gsn, Gsb / Plasmid: pETM22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13020 |
-Non-polymers , 5 types, 459 molecules
#3: Chemical | ChemComp-ATP / | ||||
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#4: Chemical | ChemComp-SCN / | ||||
#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: 2.42 Å3/Da / Density % sol: 49.17 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: 14 or 15% PEG3350, 0.2M potassium thiocyanate, 0.1M bis-tris pH 5.9. Drops were streak-seeded from crystals with calcium. |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9806 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9806 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→45 Å / Num. obs: 72676 / % possible obs: 100 % / Redundancy: 12.6 % / Net I/σ(I): 33.81 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.4→71.55 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.677 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.05 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.695 Å2
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Refinement step | Cycle: 1 / Resolution: 1.4→71.55 Å
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