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Yorodumi- PDB-3s5m: Crystal structures of falcilysin, a M16 metalloprotease from the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s5m | ||||||
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Title | Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum | ||||||
Components | Falcilysin | ||||||
Keywords | HYDROLASE / M16 metalloprotease / peptidase | ||||||
Function / homology | Function and homology information hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / chloroplast / protein processing / metalloendopeptidase activity / mitochondrial matrix / metal ion binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.55 Å | ||||||
Authors | Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T. | ||||||
Citation | Journal: To be Published Title: Crystal structures of falcilysin, a M16 metalloprotease from the malaria parasite Plasmodium falciparum Authors: Morgunova, E. / Ponpuak, M. / Istvan, E. / Popov, A. / Goldberg, D. / Eneqvist, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s5m.cif.gz | 456.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s5m.ent.gz | 371.6 KB | Display | PDB format |
PDBx/mmJSON format | 3s5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s5m_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 3s5m_full_validation.pdf.gz | 448.6 KB | Display | |
Data in XML | 3s5m_validation.xml.gz | 50 KB | Display | |
Data in CIF | 3s5m_validation.cif.gz | 77.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s5/3s5m ftp://data.pdbj.org/pub/pdb/validation_reports/s5/3s5m | HTTPS FTP |
-Related structure data
Related structure data | 3s5hC 3s5iC 3s5kC 2fgeS 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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-Components
#1: Protein | Mass: 139050.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: HB3 / Gene: flN, PF13_0322 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q76NL8 | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 11% PEG6000, 10% PEG400, 0.1M ADA, 20 mM Mg acetate, 20 mM Zn acetate, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2010 / Details: bent cylindrical mirror |
Radiation | Monochromator: single crystal Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→29.2 Å / Num. all: 866049 / Num. obs: 866049 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.51→1.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.9 / Num. unique all: 24464 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: 2FGE Resolution: 1.55→29.2 Å / SU ML: 0.19 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0.94 / Phase error: 20.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.606 Å2 / ksol: 0.365 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.1 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→29.2 Å
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Refine LS restraints |
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LS refinement shell |
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