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Yorodumi- PDB-8pz0: Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pz0 | ||||||
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Title | Intracellular leucine aminopeptidase of Pseudomonas aeruginosa PA14. | ||||||
Components | Probable cytosol aminopeptidase | ||||||
Keywords | HYDROLASE / aminopeptidase / metalloenzyme / hexamer | ||||||
Function / homology | Function and homology information bacterial leucyl aminopeptidase / leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PA14 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Simpson, M.C. / Czekster, C.M. / Harding, C.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2023 Title: Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Authors: Simpson, M.C. / Harding, C.J. / Czekster, R.M. / Remmel, L. / Bode, B.E. / Czekster, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pz0.cif.gz | 208.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pz0.ent.gz | 163.6 KB | Display | PDB format |
PDBx/mmJSON format | 8pz0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pz/8pz0 ftp://data.pdbj.org/pub/pdb/validation_reports/pz/8pz0 | HTTPS FTP |
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-Related structure data
Related structure data | 8pzmC 8pzyC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 55057.242 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PA14 (bacteria) / Strain: PA14 / Gene: pepA, PA14_14470 / Plasmid: pJ411 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q02RY8, leucyl aminopeptidase, bacterial leucyl aminopeptidase |
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-Non-polymers , 5 types, 430 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-BCT / | #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.79 Å3/Da / Density % sol: 67.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14 % PEG 3350 and 200 mM ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→45.49 Å / Num. obs: 78846 / % possible obs: 100 % / Redundancy: 36.7 % / Biso Wilson estimate: 33.95 Å2 / CC1/2: 1 / Rrim(I) all: 0.14 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 18.56 % / Rmerge(I) obs: 4.03 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3880 / CC1/2: 0.3 / Rrim(I) all: 4.141 / % possible all: 99.59 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.49 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.81 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→45.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 58.3984 Å / Origin y: 50.4129 Å / Origin z: 36.8664 Å
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Refinement TLS group | Selection details: all |