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Yorodumi- PDB-1lee: CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lee | ||||||
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Title | CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM IN COMPLEX WITH INHIBITOR RS367 | ||||||
Components | Plasmepsin 2 | ||||||
Keywords | HYDROLASE / plasmepsin / aspartic protease / plasmodium falciparum | ||||||
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 Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Asojo, O.A. / Afonina, E. / Gulnik, S.V. / Yu, B. / Erickson, J.W. / Randad, R. / Mehadjed, D. / Silva, A.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Structures of Ser205 mutant plasmepsin II from Plasmodium falciparum at 1.8 A in complex with the inhibitors rs367 and rs370. Authors: Asojo, O.A. / Afonina, E. / Gulnik, S.V. / Yu, B. / Erickson, J.W. / Randad, R. / Medjahed, D. / Silva, A.M. #1: Journal: J.Mol.Biol. / Year: 2003 Title: Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum. Authors: Asojo, O.A. / Gulnik, S.V. / Afonina, E. / Yu, B. / Ellman, J.A. / Haque, T.S. / Silva, A.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lee.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lee.ent.gz | 65.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lee.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lee_validation.pdf.gz | 759.9 KB | Display | wwPDB validaton report |
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Full document | 1lee_full_validation.pdf.gz | 768.5 KB | Display | |
Data in XML | 1lee_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 1lee_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/le/1lee ftp://data.pdbj.org/pub/pdb/validation_reports/le/1lee | HTTPS FTP |
-Related structure data
Related structure data | 1lf2C 1smeS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37079.824 Da / Num. of mol.: 1 / Fragment: Residues 123-453 / Source method: isolated from a natural source Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum) References: UniProt: P46925, plasmepsin II |
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#2: Chemical | ChemComp-R36 / |
#3: 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: 2.67 Å3/Da / Density % sol: 53.95 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 26322 / Num. obs: 23619 / % possible obs: 71 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3 / Rsym value: 0.22 / % possible all: 33 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 26322 / % possible obs: 71 % / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 33 % / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SME Resolution: 1.9→34.92 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 600592.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 300 Å2 / ksol: 0.482127 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→34.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / Rfactor Rfree: 0.296 / Rfactor Rwork: 0.264 |