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Yorodumi- PDB-3b35: Crystal structure of the M180A mutant of the aminopeptidase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b35 | ||||||
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Title | Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus | ||||||
Components | Bacterial leucyl aminopeptidase | ||||||
Keywords | HYDROLASE / alpha beta / Aminopeptidase / Metal-binding / Protease / Secreted / Zinc / Zymogen | ||||||
Function / homology | Function and homology information bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Vibrio proteolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å | ||||||
Authors | Ataie, N.J. / Hoang, Q.Q. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus. Authors: Ataie, N.J. / Hoang, Q.Q. / Zahniser, M.P. / Tu, Y. / Milne, A. / Petsko, G.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b35.cif.gz | 150.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b35.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 3b35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/3b35 ftp://data.pdbj.org/pub/pdb/validation_reports/b3/3b35 | HTTPS FTP |
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-Related structure data
Related structure data | 3b3cC 3b3sC 3b3tC 3b3vC 3b3wC 3b7iC 1ampS 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 on special symmetry positions |
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Details | Authors state that the biological unit of this protein is unknown. |
-Components
#1: Protein | Mass: 31367.232 Da / Num. of mol.: 1 / Fragment: Residues 107-397 / Mutation: M286A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Strain: DSM 30189 / IFO 13287 / LMG 3772 / NCIMB 1326 / Gene: AAP / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q01693, bacterial leucyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / #4: Chemical | #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: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9001 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9001 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→41 Å / Num. obs: 122065 / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.059 |
Reflection shell | Highest resolution: 1.1 Å / Mean I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1AMP Resolution: 1.1→41 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.825 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.03 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.1→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Total num. of bins used: 20
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