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Yorodumi- PDB-3fns: Crystal structure of histo-aspartic protease (HAP) from Plasmodiu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fns | ||||||
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Title | Crystal structure of histo-aspartic protease (HAP) from Plasmodium Falciparum | ||||||
Components | HAP protein | ||||||
Keywords | HYDROLASE / Histo-aspartic protease / HAP / Plasmepsin / Aspartic protease / HORMONE | ||||||
Function / homology | Function and homology information MHC class II antigen presentation / plasmepsin II / acquisition of nutrients from host / Neutrophil degranulation / vacuolar lumen / food vacuole / aspartic-type endopeptidase activity / proteolysis / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Bhaumik, P. / Gustchina, A. / Wlodawer, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum. Authors: Bhaumik, P. / Xiao, H. / Parr, C.L. / Kiso, Y. / Gustchina, A. / Yada, R.Y. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fns.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fns.ent.gz | 111.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fns.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/3fns ftp://data.pdbj.org/pub/pdb/validation_reports/fn/3fns | HTTPS FTP |
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-Related structure data
Related structure data | 3fntC 3fnuC 2anlS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 0 - 326 / Label seq-ID: 6 - 330
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Details | Two molecules of histo-aspartic protease (HAP) are present in the asymmetric unit. Two molecules form a tight dimer related by a non-crystallographic symmetry. |
-Components
#1: Protein | Mass: 37435.250 Da / Num. of mol.: 2 / Fragment: Histo-aspartic protease (HAP) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: HAP, PF14_0078 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q8IM15 #2: Chemical | ChemComp-ZN / #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: 2.68 Å3/Da / Density % sol: 54.02 % Description: AUTHORS STATE THAT THE VALUE OF RMERGE IN THE HIGHEST RESOLUTION SHELL IS HIGH DUE TO POORLY DIFFRACTING CRYSTAL/HIGH SYMMETRY SPACE GROUP/ HIGHLY REDUNDANT DATA. CRYSTAL HAS SUFFERED SOME RADIATION DAMAGE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 10% PEG 3000, 0.2M Zinc acetate, 0.1M sodium acetate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→40 Å / Num. all: 28973 / Num. obs: 28895 / % possible obs: 99.7 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.093 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.822 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3120 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ANL Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.239 / SU ML: 0.233 / Cross valid method: THROUGHOUT / ESU R: 0.5 / ESU R Free: 0.3 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2591 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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