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Yorodumi- PDB-2ek9: Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ek9 | ||||||
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Title | Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin | ||||||
Components | Aminopeptidase | ||||||
Keywords | HYDROLASE / METALLOPROTEINASE | ||||||
Function / homology | Function and homology information metalloexopeptidase activity / aminopeptidase activity / proteolysis / metal ion binding Similarity search - Function | ||||||
Biological species | Aneurinibacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Akioka, M. / Nakano, H. / Watanabe, K. | ||||||
Citation | Journal: To be published Title: Structural characterization of a novel bacterial aminopeptidase with an apical domain from aneurinibacillus sp. strain AM-1 Authors: Akioka, M. / Nakano, H. / Tsujimoto, Y. / Matsui, H. / Nakatsu, T. / Kato, H. / Watanabe, K. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Overexpression, purification, crystallization and preliminary X-ray crystallographic studies of a proline-specific aminopeptidase from Aneurinibacillus sp. strain AM-1 Authors: Akioka, M. / Nakano, H. / Horikiri, A. / Tsujimoto, Y. / Matsui, H. / Shimizu, T. / Nakatsu, T. / Kato, H. / Watanabe, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ek9.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ek9.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 2ek9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/2ek9 ftp://data.pdbj.org/pub/pdb/validation_reports/ek/2ek9 | HTTPS FTP |
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-Related structure data
Related structure data | 2ek8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45289.699 Da / Num. of mol.: 1 / Fragment: Residues 1-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aneurinibacillus sp. (bacteria) / Strain: AM-1 / Plasmid: PET-11A / Production host: Escherichia coli (E. coli) / References: UniProt: A2V759 | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-BES / | #4: Chemical | ChemComp-IPA / | #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: 2.74 Å3/Da / Density % sol: 55.09 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion / pH: 5.8 Details: 13% PEG 8000, 0.1M MES-NaOH, 0.2M Zinc acetate, pH 5.8, VAPOR DIFFUSION, temperature 299K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Aug 29, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→15 Å / Num. obs: 35820 / % possible obs: 99.8 % / Redundancy: 4.75 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.97→2.08 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 4.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EK8 Resolution: 1.97→15 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2014166.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 59.7327 Å2 / ksol: 0.393232 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.97→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.09 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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