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Yorodumi- PDB-4qpe: Crystal structure of Aminopeptidase N in complex with N-cyclohexy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qpe | ||||||
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Title | Crystal structure of Aminopeptidase N in complex with N-cyclohexyl-1,2-diaminoethylphosphonic acid | ||||||
Components | Aminopeptidase N | ||||||
Keywords | HYDROLASE / alanine aminopeptidase / Aminopeptidase N / M1 family peptidases / N-cyclohexyl-1 / 2-diaminoethylphosphonic acid | ||||||
Function / homology | Function and homology information membrane alanyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | Neisseria meningitidis MC58 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å | ||||||
Authors | Nocek, B. / Mulligan, R. / Berlicki, L. / Vassilious, S. / Mucha, A. / Joachimiak, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases. Authors: Vassiliou, S. / Weglarz-Tomczak, E. / Berlicki, L. / Paweczak, M. / Nocek, B. / Mulligan, R. / Joachimiak, A. / Mucha, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qpe.cif.gz | 514.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qpe.ent.gz | 428.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qpe_validation.pdf.gz | 448.8 KB | Display | wwPDB validaton report |
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Full document | 4qpe_full_validation.pdf.gz | 449.3 KB | Display | |
Data in XML | 4qpe_validation.xml.gz | 36.7 KB | Display | |
Data in CIF | 4qpe_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qp/4qpe ftp://data.pdbj.org/pub/pdb/validation_reports/qp/4qpe | HTTPS FTP |
-Related structure data
Related structure data | 4qhpC 4qirC 4qmeC 4quoC 2gtqS 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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Unit cell |
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-Components
#1: Protein | Mass: 98962.633 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria meningitidis MC58 (bacteria) / Gene: pepN, NMB1416 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9JYV4, membrane alanyl aminopeptidase | ||
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#2: Chemical | ChemComp-37E / [( | ||
#3: Chemical | ChemComp-ZN / | ||
#4: Chemical | ChemComp-SO4 / #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: 2.84 Å3/Da / Density % sol: 56.69 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 2.0 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2013 / Details: mirrors |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.062 Å / Num. all: 71931 / Num. obs: 71931 / % possible obs: 98.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2GTQ Resolution: 2.004→28.062 Å / SU ML: 0.23 / σ(F): 1.99 / σ(I): 3 / Phase error: 21.22 / 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: 2.004→28.062 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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