+Open data
-Basic information
Entry | Database: PDB / ID: 5wze | ||||||
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Title | The structure of Pseudomonas aeruginosa aminopeptidase PepP | ||||||
Components | Aminopeptidase PXaa-Pro aminopeptidase | ||||||
Keywords | HYDROLASE / aminopeptidase / Pseudomonas aeruginosa / pathogenicity | ||||||
Function / homology | Function and homology information metalloaminopeptidase activity / : / aminopeptidase activity / manganese ion binding / peptidase activity / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å | ||||||
Authors | Bao, R. / Peng, C.T. / Liu, L. / He, L.H. / Li, C.C. / Li, T. / Shen, Y.L. / Zhu, Y.B. / Song, Y.J. | ||||||
Citation | Journal: Front Microbiol / Year: 2017 Title: Structure-Function Relationship of Aminopeptidase P from Pseudomonas aeruginosa. Authors: Peng, C.T. / Liu, L. / Li, C.C. / He, L.H. / Li, T. / Shen, Y.L. / Gao, C. / Wang, N.Y. / Xia, Y. / Zhu, Y.B. / Song, Y.J. / Lei, Q. / Yu, L.T. / Bao, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wze.cif.gz | 386.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wze.ent.gz | 311.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/5wze ftp://data.pdbj.org/pub/pdb/validation_reports/wz/5wze | HTTPS FTP |
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-Related structure data
Related structure data | 1az9 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 50845.570 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: pepP, PA5224 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9HTW6 |
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-Non-polymers , 10 types, 1192 molecules
#2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-PRO / #6: Chemical | #7: Chemical | ChemComp-CA / #8: Chemical | ChemComp-MN / #9: Chemical | ChemComp-PGE / | #10: Chemical | ChemComp-EDO / #11: 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: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG400, 100 mM sodium cacodylate pH 6.5, 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.783→48.01 Å / Num. obs: 194517 / % possible obs: 99 % / Redundancy: 8.9 % / Net I/σ(I): 19.714 |
Reflection shell | Resolution: 1.783→1.8275 Å / Rmerge(I) obs: 0.709 / Num. unique obs: 18600 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AZ9 1az9 Resolution: 1.783→48.008 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.783→48.008 Å
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Refine LS restraints |
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LS refinement shell |
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