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Yorodumi- PDB-3kzw: Crystal structure of cytosol aminopeptidase from Staphylococcus a... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 3kzw | ||||||
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| Title | Crystal structure of cytosol aminopeptidase from Staphylococcus aureus COL | ||||||
Components | Cytosol aminopeptidase | ||||||
Keywords | HYDROLASE / Cytosol aminopeptidase / Aminopeptidase / Manganese / Metal-binding / Protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
| Function / homology | Function and homology informationleucyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / proteolysis / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Hattne, J. / Dubrovska, I. / Halavaty, A. / Minasov, G. / Scott, P. / Shuvalova, L. / Winsor, J. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 3kzw.cif.gz | 1 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb3kzw.ent.gz | 868.6 KB | Display | PDB format |
| PDBx/mmJSON format | 3kzw.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/3kzw ftp://data.pdbj.org/pub/pdb/validation_reports/kz/3kzw | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 1gytS S: Starting model for refinement |
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| Similar structure data | |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
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Components
| #1: Protein | Mass: 56930.312 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: COL / Gene: SACOL0945 / Plasmid: pMCSG19c / Production host: ![]() References: UniProt: Q5HHE3, UniProt: A0A0H2WYH0*PLUS, leucyl aminopeptidase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.45 % |
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| Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 70% MPD, 0.1M HEPES, pH 7.5, 0.5M sodium chloride, 0.01M Tris-HCl, pH 8.3, JCSG+, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
| Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2008 / Details: Beryllium lenses |
| Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
| Reflection | Resolution: 2.7→44.62 Å / Num. all: 207017 / Num. obs: 204154 / % possible obs: 98.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 9.19 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB entry 1gyt Resolution: 2.7→44.62 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.893 / SU B: 28.362 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The upper resolution limit was determined by an informativity criterium. 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 4.572 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.7→44.62 Å
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| Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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