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Yorodumi- PDB-4j3b: A naturally variable residue in the S1 subsite of M1-family amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j3b | ||||||
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Title | A naturally variable residue in the S1 subsite of M1-family aminopeptidases modulates catalytic properties and promotes functional specialization | ||||||
Components | M1 family aminopeptidase | ||||||
Keywords | HYDROLASE / Protease / Peptides | ||||||
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 / chloroplast / proteolysis / zinc ion binding ...symbiont-containing vacuole membrane / vacuolar lumen / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / food vacuole / dipeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / chloroplast / proteolysis / zinc ion binding / membrane / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dalal, S. / Ragheb, D.R.T. / Schubot, F.D. / Klemba, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: A naturally variable residue in the s1 subsite of m1 family aminopeptidases modulates catalytic properties and promotes functional specialization. Authors: Dalal, S. / Ragheb, D.R. / Schubot, F.D. / Klemba, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j3b.cif.gz | 204 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j3b.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 4j3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j3b ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j3b | HTTPS FTP |
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-Related structure data
Related structure data | 3ebiS 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: 103602.516 Da / Num. of mol.: 1 / Fragment: UNP residues 197-1083 / Mutation: V459P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: FcB1/Columbia / Gene: P.falciparum / Production host: Escherichia coli (E. coli) References: UniProt: O96935, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases |
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#2: Chemical | ChemComp-ARG / |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-MG / |
#5: 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: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Method: vapor diffusion / Details: VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2011 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 46026 / % possible obs: 100 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3EBI Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.513 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.335 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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