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Yorodumi- PDB-3n5i: Crystal structure of the precursor (S250A mutant) of the N-termin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n5i | ||||||
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Title | Crystal structure of the precursor (S250A mutant) of the N-terminal beta-aminopeptidase BapA | ||||||
Components | Beta-peptidyl aminopeptidase | ||||||
Keywords | HYDROLASE / Ntn hydrolase / alpha-beta-beta-alpha sandwich / beta-aminopeptidase / beta-peptide | ||||||
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: 1.8 Å | ||||||
Authors | Merz, T. / Heck, T. / Geueke, B. / Kohler, H.-P. / Gruetter, M.G. | ||||||
Citation | Journal: Structure / Year: 2012 Title: Autoproteolytic and catalytic mechanisms for the beta-aminopeptidase BapA--a member of the Ntn hydrolase family. Authors: Merz, T. / Heck, T. / Geueke, B. / Mittl, P.R. / Briand, C. / Seebach, D. / Kohler, H.P. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n5i.cif.gz | 294.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n5i.ent.gz | 236.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3n5i_validation.pdf.gz | 471.5 KB | Display | wwPDB validaton report |
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Full document | 3n5i_full_validation.pdf.gz | 479.3 KB | Display | |
Data in XML | 3n5i_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 3n5i_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n5/3n5i ftp://data.pdbj.org/pub/pdb/validation_reports/n5/3n5i | HTTPS FTP |
-Related structure data
Related structure data | 3n2wSC 3n33C 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: 38618.836 Da / Num. of mol.: 4 / Mutation: S250A 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-SO4 / #4: 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: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.0 - 1.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-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 22, 2008 / Details: dynamically bendable mirror |
Radiation | Monochromator: 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: 1.8→29.399 Å / Num. obs: 131688 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 4.4 % / Rmerge(I) obs: 0.098 / Rsym value: 0.071 / Net I/σ(I): 15.64 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.45 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.96 / Num. unique all: 19497 / Rsym value: 0.473 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: single chain of PDB code 3N2W, w/o aa 231-250 Resolution: 1.8→29.394 Å / SU ML: 0.19 / 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: 40.421 Å2 / ksol: 0.373 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→29.394 Å
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Refine LS restraints |
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LS refinement shell |
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