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- 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 | ||||||
![]() | Cytosol aminopeptidase | ||||||
![]() | HYDROLASE / Cytosol aminopeptidase / Aminopeptidase / Manganese / Metal-binding / Protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | ![]() leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / manganese ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hattne, J. / Dubrovska, I. / Halavaty, A. / Minasov, G. / Scott, P. / Shuvalova, L. / Winsor, J. / Otwinowski, Z. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 868.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 554.5 KB | Display | ![]() |
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Full document | ![]() | 574.3 KB | Display | |
Data in XML | ![]() | 177.4 KB | Display | |
Data in CIF | ![]() | 247.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gytS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]() Starting 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 |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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