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Yorodumi- PDB-5bwy: Structure of proplasmepsin II from Plasmodium falciparum, Space G... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5bwy | ||||||
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Title | Structure of proplasmepsin II from Plasmodium falciparum, Space Group P43212 | ||||||
Components | Plasmepsin-2 | ||||||
Keywords | HYDROLASE / malaria | ||||||
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 / molecular replacement / Resolution: 2.644 Å | ||||||
Authors | Recacha, R. / Akopjana, I. / Tars, K. / Jaudzems, K. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016 Title: Crystal structure of Plasmodium falciparum proplasmepsin IV: the plasticity of proplasmepsins. Authors: Recacha, R. / Jaudzems, K. / Akopjana, I. / Jirgensons, A. / Tars, K. #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 | 5bwy.cif.gz | 167.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bwy.ent.gz | 133.2 KB | Display | PDB format |
PDBx/mmJSON format | 5bwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bwy_validation.pdf.gz | 421.2 KB | Display | wwPDB validaton report |
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Full document | 5bwy_full_validation.pdf.gz | 427.7 KB | Display | |
Data in XML | 5bwy_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5bwy_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/5bwy ftp://data.pdbj.org/pub/pdb/validation_reports/bw/5bwy | HTTPS FTP |
-Related structure data
Related structure data | 5jodC 1pfzS S: Starting model for refinement C: citing same article (ref.) |
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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: 42374.969 Da / Num. of mol.: 1 / Fragment: UNP residues 78-453 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFAG_05140 / Plasmid: pET3A / Production host: Escherichia coli (E. coli) / References: UniProt: W7FL77, UniProt: P46925*PLUS |
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#2: 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: 2.73 Å3/Da / Density % sol: 54.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M Sodium Citrate, 0.1 M Sodium Acetate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.972 Å |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: May 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.972 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→44.7 Å / Num. all: 14252 / Num. obs: 14252 / % possible obs: 100 % / Redundancy: 2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.64→2.76 Å / Redundancy: 5 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PFZ Resolution: 2.644→44.69 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.46 / 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: 2.644→44.69 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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