+Open data
-Basic information
Entry | Database: PDB / ID: 8c47 | |||||||||
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Title | Leishmania ATP-actin monomer in complex with Leishmania profilin | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Actin / profilin / leishmania / cytoskeleton | |||||||||
Function / homology | Function and homology information kinetoplast / sequestering of actin monomers / actin monomer binding / cell cortex / endonuclease activity / cytoskeleton / chromatin remodeling Similarity search - Function | |||||||||
Biological species | Leishmania major (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Kogan, K. / Kotila, T. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2024 Title: Leishmania profilin interacts with actin through an unusual structural mechanism to control cytoskeletal dynamics in parasites. Authors: Vizcaino-Castillo, A. / Kotila, T. / Kogan, K. / Yanase, R. / Como, J. / Antenucci, L. / Michelot, A. / Sunter, J.D. / Lappalainen, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8c47.cif.gz | 263.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8c47.ent.gz | 175.6 KB | Display | PDB format |
PDBx/mmJSON format | 8c47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/8c47 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/8c47 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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 BA
#1: Protein | Mass: 16185.040 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LMJF_32_0520 / Plasmid: pPL1718 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4Q5N1 |
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#2: Protein | Mass: 41932.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania major (eukaryote) / Gene: ACT, LMJF_04_1230 / Plasmid: pPL1698 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9U1E8 |
-Non-polymers , 4 types, 247 molecules
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-CA / | #6: 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: 2.76 Å3/Da / Density % sol: 55.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 5.5, PEG4000 26% (w/v) and 0.2 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→33.59 Å / Num. obs: 32700 / % possible obs: 99.83 % / Redundancy: 7.7 % / Biso Wilson estimate: 49.55 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.034 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 1.234 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2799 / CC1/2: 0.799 / Rpim(I) all: 0.472 / % possible all: 99.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.16 Å / SU ML: 0.2519 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7991 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.46 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→32.16 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 | Refine-ID: X-RAY DIFFRACTION
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