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Yorodumi- PDB-3nfb: Crystal structure of the N-terminal beta-aminopeptidase BapA in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nfb | ||||||
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Title | Crystal structure of the N-terminal beta-aminopeptidase BapA in complex with hydrolyzed ampicillin | ||||||
Components | Beta-peptidyl aminopeptidase | ||||||
Keywords | Hydrolase/Inhibitor / Ntn-hydrolase / alpha-beta-beta-alpha sandwich / beta-peptide cleaving enzyme / Hydrolase-Inhibitor 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: 1.85 Å | ||||||
Authors | Merz, T. / Heck, T. / Geueke, B. / Kohler, H.-P.E. / Gruetter, M.G. | ||||||
Citation | Journal: To be Published Title: Crystal structure 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 | 3nfb.cif.gz | 302.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nfb.ent.gz | 244.4 KB | Display | PDB format |
PDBx/mmJSON format | 3nfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nfb_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 3nfb_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 3nfb_validation.xml.gz | 63.1 KB | Display | |
Data in CIF | 3nfb_validation.cif.gz | 93.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfb ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfb | HTTPS FTP |
-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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1 |
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Unit cell |
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Details | tetramer of heterodimers |
-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) 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-OAE / ( #4: Chemical | ChemComp-SO4 / #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: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 15mg/ml, 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: Sep 16, 2009 / Details: dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→49.3 Å / Num. obs: 137090 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.78 % / Rmerge(I) obs: 0.11 / Rsym value: 0.086 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.76 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.98 / Num. unique all: 10556 / Rsym value: 0.455 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3N2W Resolution: 1.85→49.3 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: 49.383 Å2 / ksol: 0.371 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.85→49.3 Å
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Refine LS restraints |
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LS refinement shell |
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