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Yorodumi- PDB-3fh4: Crystal Structure of Recombinant Vibrio proteolyticus aminopeptidase -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fh4 | ||||||
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Title | Crystal Structure of Recombinant Vibrio proteolyticus aminopeptidase | ||||||
Components | Bacterial leucyl aminopeptidase | ||||||
Keywords | HYDROLASE / Recombinant Vibrio proteolyticus aminopeptidase / 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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Yong, W. / Kim, J.-J.P. / Hartley, M. / Bennett, B. | ||||||
Citation | Journal: Protein Expr.Purif. / Year: 2009 Title: Heterologous expression and purification of Vibrio proteolyticus (Aeromonas proteolytica) aminopeptidase: a rapid protocol Authors: Hartley, M. / Bennett, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fh4.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fh4.ent.gz | 53.4 KB | Display | PDB format |
PDBx/mmJSON format | 3fh4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/3fh4 ftp://data.pdbj.org/pub/pdb/validation_reports/fh/3fh4 | HTTPS FTP |
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-Related structure data
Related structure data | 2iq6S 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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-Components
#1: Protein | Mass: 32238.150 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Strain: IFO13287 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) References: UniProt: Q01693, bacterial leucyl aminopeptidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-TRS / | #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: 2.46 Å3/Da / Density % sol: 50.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: VpAP (0.5 mM) in 10 mM Tris buffer, pH 8.0, containing 10 mM KSCN and 400 mM NaCl was equilibrated with 100 mM Tris buffer, pH 8.0, containing 100 mM KSCN and 4.5 M NaCl, VAPOR DIFFUSION, ...Details: VpAP (0.5 mM) in 10 mM Tris buffer, pH 8.0, containing 10 mM KSCN and 400 mM NaCl was equilibrated with 100 mM Tris buffer, pH 8.0, containing 100 mM KSCN and 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 7, 2008 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→41.89 Å / Num. obs: 23158 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 21 % / Rsym value: 0.135 |
Reflection shell | Highest resolution: 1.95 Å / Redundancy: 21 % / Mean I/σ(I) obs: 31.5 / Rsym value: 0.515 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2IQ6 Resolution: 1.95→26.03 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.355 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.151 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.414 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→26.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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