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Yorodumi- PDB-4z22: structure of plasmepsin II from Plasmodium Falciparum complexed w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z22 | ||||||
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Title | structure of plasmepsin II from Plasmodium Falciparum complexed with inhibitor DR718A | ||||||
Components | Plasmepsin-2 | ||||||
Keywords | HYDROLASE / plasmepsin II / malaria / inhibitor | ||||||
Function / homology | Function and homology information cytostome / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / vacuolar membrane / aspartic-type endopeptidase activity / proteolysis / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Recacha, R. / Leitans, J. / Tars, K. / Jaudzems, K. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Fragment-Based Discovery of 2-Aminoquinazolin-4(3H)-ones As Novel Class Nonpeptidomimetic Inhibitors of the Plasmepsins I, II, and IV. Authors: Rasina, D. / Otikovs, M. / Leitans, J. / Recacha, R. / Borysov, O.V. / Kanepe-Lapsa, I. / Domraceva, I. / Pantelejevs, T. / Tars, K. / Blackman, M.J. / Jaudzems, K. / Jirgensons, A. #1: Journal: Nat. Struct. Biol. / Year: 1999 Title: Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from plasmodium falciparum. Authors: Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N. #2: Journal: J. Mol. Biol. / Year: 2003 Title: Structural insights into the activation of P. vivax plasmepsin. Authors: Bernstein, N.K. / Cherney, M.M. / Yowell, C.A. / Dame, J.B. / James, M.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z22.cif.gz | 277.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z22.ent.gz | 226.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z22.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/4z22 ftp://data.pdbj.org/pub/pdb/validation_reports/z2/4z22 | HTTPS FTP |
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-Related structure data
Related structure data | 2bjuS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36909.617 Da / Num. of mol.: 2 / Fragment: UNP residues 125-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFAG_05140 / Production host: Escherichia coli (E. coli) / References: UniProt: W7FL77, UniProt: P46925*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.16 Å3/Da / Density % sol: 42.95 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M CITRIC ACID, PH 4.5, 0.4M AMMONIUM ACETATE, 21% PEG 3350, PROTEIN 10 MG/ML, 10 MM INHIBITOR (in 100% DMSO) PH range: 4.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 19, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.62→87.345 Å / Num. all: 19551 / Num. obs: 19551 / % possible obs: 99.3 % / Redundancy: 3.4 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.104 / Rsym value: 0.088 / Net I/av σ(I): 7.281 / Net I/σ(I): 9.1 / Num. measured all: 66480 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BJU Resolution: 2.62→41.664 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→41.664 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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