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Yorodumi- PDB-5y3i: Crystal structure of Plasmodium falciparum aminopeptidase N in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5y3i | ||||||
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Title | Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-methylbenzyl)ureido)pentanamide | ||||||
Components | M1 family aminopeptidase | ||||||
Keywords | HYDROLASE / M1-family / Aminopeptidase | ||||||
Function / homology | Function and homology information symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å | ||||||
Authors | Marapaka, A.K. / Zhang, Y. / Addlagatta, A. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-N-hydroxy-4-methyl-2-(3-(3-methylbenzyl)ureido)pentanamide Authors: Marapaka, A.K. / Addlagatta, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5y3i.cif.gz | 214.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5y3i.ent.gz | 163.3 KB | Display | PDB format |
PDBx/mmJSON format | 5y3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/5y3i ftp://data.pdbj.org/pub/pdb/validation_reports/y3/5y3i | HTTPS FTP |
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-Related structure data
Related structure data | 4x2uS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 106291.477 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 195-1085 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: isolate FcB1 / Columbia / Production host: Escherichia coli (E. coli) References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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-Non-polymers , 5 types, 634 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-8N3 / ( | #5: Chemical | ChemComp-GOL / #6: 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: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris, pH8.5, 0.2M Magnesium chloride, 24% PEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 4, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.73→25 Å / Num. obs: 95904 / % possible obs: 99.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.014 / Rrim(I) all: 0.035 / Χ2: 1.048 / Net I/σ(I): 42.4 / Num. measured all: 602753 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.364
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4X2U Resolution: 1.73→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.1748 / FOM work R set: 0.888 / SU B: 1.742 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1035 / SU Rfree: 0.1028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 65.76 Å2 / Biso mean: 18.647 Å2 / Biso min: 7.76 Å2
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Refinement step | Cycle: final / Resolution: 1.73→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.729→1.774 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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