+Open data
-Basic information
Entry | Database: PDB / ID: 1pfz | ||||||
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Title | PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM | ||||||
Components | PROPLASMEPSIN II | ||||||
Keywords | ASPARTIC PROTEASE ZYMOGEN / ASPARTIC PROTEINASE ZYMOGEN / HEMOGLOBINASE / MALARIA / HYDROLASE / ASPARTYL PROTEASE / GLYCOPROTEIN | ||||||
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: 1.85 Å | ||||||
Authors | Bernstein, N.K. / Cherney, M.M. / Loetscher, H. / Ridley, R.G. / James, M.N.G. | ||||||
Citation | 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. #1: Journal: FEBS Lett. / Year: 1994 Title: High Level Expression and Characterisation of Plasmepsin II, an Aspartic Proteinase from Plasmodium Falciparum Authors: Hill, J. / Tyas, L. / Phylip, L.H. / Kay, J. / Dunn, B.M. / Berry, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pfz.cif.gz | 307.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pfz.ent.gz | 257.8 KB | Display | PDB format |
PDBx/mmJSON format | 1pfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pfz_validation.pdf.gz | 479.4 KB | Display | wwPDB validaton report |
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Full document | 1pfz_full_validation.pdf.gz | 508.8 KB | Display | |
Data in XML | 1pfz_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 1pfz_validation.cif.gz | 85.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/1pfz ftp://data.pdbj.org/pub/pdb/validation_reports/pf/1pfz | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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3 |
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6 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 42733.336 Da / Num. of mol.: 4 Mutation: 76 RESIDUES AT THE N-TERMINUS OF THE PROSEGMENT (1P - 76P) HAVE BEEN TRUNCATED, 3 RESIDUES (GLY-ARG-GLY) HAVE BEEN ADDED AT THE N-TERMINUS AS AN ARTIFACT OF THE EXPRESSION SYSTEM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Cell line: BL21 / Organelle: DIGESTIVE VACUOLE / Plasmid: PBLUESCRIPT KS+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P46925, plasmepsin II #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Sequence details | NOMENCLATURE: THE PROSEGMENT RESIDUES HAVE INSERTION CODE P (78/79 P - 118/124 P). NUMBERING FOR ...NOMENCLATU | |
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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: 2.5 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 105 K / Method: vapor diffusion, sitting dropDetails: 2 microlitter of protein splution was mixed with 7 microlitter of reservoir solution PH range low: 8 / PH range high: 7.5 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jul 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. obs: 114943 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 3 / % possible all: 91.5 |
Reflection shell | *PLUS % possible obs: 91.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2505951.19 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: BULK SOLVENT MODEL USED DATA CUTOFF HIGH (ABS(F)) : 2505951.19 DATA CUTOFF LOW (ABS(F)) : 0.000000
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Solvent computation | Solvent model: FLAT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.276 |