+Open data
-Basic information
Entry | Database: PDB / ID: 2igx | ||||||
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Title | Achiral, Cheap and Potent Inhibitors of Plasmepsins II | ||||||
Components | Plasmepsin-2 | ||||||
Keywords | HYDROLASE / achiral 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 Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Prade, L. | ||||||
Citation | Journal: Chemmedchem / Year: 2006 Title: Achiral, Cheap, and Potent Inhibitors of Plasmepsins I, II, and IV. Authors: Boss, C. / Corminboeuf, O. / Grisostomi, C. / Meyer, S. / Jones, A.F. / Prade, L. / Binkert, C. / Fischli, W. / Weller, T. / Bur, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2igx.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2igx.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 2igx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ig/2igx ftp://data.pdbj.org/pub/pdb/validation_reports/ig/2igx | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 36953.734 Da / Num. of mol.: 1 / 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-A1T / |
#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: 2.77 Å3/Da / Density % sol: 55.62 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 15, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→51.57 Å / Num. all: 44941 / Num. obs: 44941 / % possible obs: 97.5 % / Observed criterion σ(F): 266039 / Observed criterion σ(I): 266039 / Redundancy: 5.9 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.095 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.2 / Num. unique all: 6360 / Rsym value: 0.48 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→50.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.181 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.11 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.029 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→50.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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