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Yorodumi- PDB-3ndv: Crystal structure of the N-terminal beta-aminopeptidase BapA in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ndv | ||||||
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Title | Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with ampicillin | ||||||
Components | Beta-peptidyl aminopeptidase | ||||||
Keywords | HYDROLASE/ANTIBIOTIC / Ntn-hydrolase / beta-aminopeptidase / beta-peptide / alpha-beta-beta-alpha sandwich / N-terminal beta-aminopeptidase / HYDROLASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information beta-peptidyl aminopeptidase / aminopeptidase activity / periplasmic space / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | Sphingosinicella xenopeptidilytica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Merz, T. / Heck, T. / Geueke, B. / Kohler, H.-P.E. / Gruetter, M.G. | ||||||
Citation | Journal: To be Published Title: Crystal structures and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family Authors: Heck, T. / Merz, T. / Geueke, B. / Gruetter, M.G. / Kohler, H.-P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ndv.cif.gz | 299.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndv.ent.gz | 241.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ndv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndv ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndv | HTTPS FTP |
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-Related structure data
Related structure data | 3n2wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 38634.836 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingosinicella xenopeptidilytica (bacteria) Strain: 3-2W4 / Gene: bapA / Plasmid: pYBapA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q52VH2 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-AIC / ( #4: Chemical | #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: 2.61 Å3/Da / Density % sol: 52.88 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15mg/ml protein, 1.5M ammonium sulfate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2009 / Details: dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 172088 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Rmerge(I) obs: 0.16 / Rsym value: 0.116 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / Num. unique all: 70374 / Rsym value: 0.581 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N2W Resolution: 1.7→48.835 Å / SU ML: 0.18 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.99 / 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 / Bsol: 60.428 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→48.835 Å
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Refine LS restraints |
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LS refinement shell |
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