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Yorodumi- PDB-4r1e: Crystal Structure of MTIP from Plasmodium falciparum in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r1e | ||||||
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Title | Crystal Structure of MTIP from Plasmodium falciparum in complex with a peptide-fragment chimera | ||||||
Components |
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Keywords | PROTEIN BINDING/INHIBITOR / CALMODULIN-LIKE / PROTEIN BINDING / MYOSIN MOTOR / FRAGMENT PEPTIDE / MEMBRANE / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | Function and homology information pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity ...pellicle / glideosome / inner membrane pellicle complex / mitotic actomyosin contractile ring assembly / vesicle transport along actin filament / myosin complex / myosin II complex / microfilament motor activity / myosin heavy chain binding / cytoskeletal motor activity / actin filament organization / actin filament binding / actin cytoskeleton / actin binding / vesicle / calcium ion binding / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Plasmodium falciparum Isolate 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Douse, C.H. / Vrielink, N. / Cota, E. / Tate, E.W. | ||||||
Citation | Journal: Chemmedchem / Year: 2015 Title: Targeting a Dynamic Protein-Protein Interaction: Fragment Screening against the Malaria Myosin A Motor Complex. Authors: Douse, C.H. / Vrielink, N. / Wenlin, Z. / Cota, E. / Tate, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r1e.cif.gz | 46.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r1e.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 4r1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r1e_validation.pdf.gz | 435.1 KB | Display | wwPDB validaton report |
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Full document | 4r1e_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 4r1e_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4r1e_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1e ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1e | HTTPS FTP |
-Related structure data
Related structure data | 4aomS 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
#1: Protein | Mass: 16498.234 Da / Num. of mol.: 1 / Fragment: unp residues 61-204 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: Isolate 3D7 / Gene: MTIP, PFL2225w / Plasmid: pRSETA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8I4W8 |
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#2: Protein/peptide | Mass: 1741.176 Da / Num. of mol.: 1 / Fragment: unp residues 803-816 / Source method: obtained synthetically Source: (synth.) Plasmodium falciparum Isolate 3D7 (eukaryote) References: UniProt: Q8IDR3 |
#3: Chemical | ChemComp-3EC / |
#4: Water | ChemComp-HOH / |
Sequence details | GLY802 IS NOT PART OF THE NATURAL SEQUENCE OF THE PROTEIN FROM WHICH THE PEPTIDE IS DERIVED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M ammonium sulfate, 20% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: Pilatus 2M / Detector: CCD / Date: Apr 23, 2012 |
Radiation | Monochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→44.93 Å / Num. all: 11020 / Num. obs: 11020 / % possible obs: 97.6 % / Redundancy: 3 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.98→2.09 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.106 / Mean I/σ(I) obs: 6.9 / Num. unique all: 1578 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AOM Resolution: 1.98→44.93 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.664 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.273 Å2
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Refinement step | Cycle: LAST / Resolution: 1.98→44.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.981→2.032 Å / Total num. of bins used: 20
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