+Open data
-Basic information
Entry | Database: PDB / ID: 1fye | ||||||
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Title | Aspartyl Dipeptidase (Anisotropic B-Factor Refinement) | ||||||
Components | ASPARTYL DIPEPTIDASE | ||||||
Keywords | HYDROLASE / serine protease / peptidase / catalytic triad / strand-helix motif | ||||||
Function / homology | Function and homology information dipeptidase E / dipeptidase activity / serine-type peptidase activity / proteolysis / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å | ||||||
Authors | Hakansson, K. / Wang, A.H.-J. / Miller, C.G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad. Authors: Hakansson, K. / Wang, A.H. / Miller, C.G. #1: Journal: J.Bacteriol. / Year: 2000 Title: Peptidase E, a peptidase specific for N-terminal aspartic dipeptides, is a serine hydrolase Authors: Lassy, R.A. / Miller, C.G. #2: Journal: J.Bacteriol. / Year: 1994 Title: Cloning and nucleotide sequence of the cyclic AMP receptor protein-regulated Salmonella typhimurium pepE gene and crystallization of its product, an alpha-aspartyl dipeptidase Authors: Conlin, C.A. / Hakansson, K. / Liljas, A. / Miller, C.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fye.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fye.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 1fye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fye_validation.pdf.gz | 365.3 KB | Display | wwPDB validaton report |
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Full document | 1fye_full_validation.pdf.gz | 367.7 KB | Display | |
Data in XML | 1fye_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | 1fye_validation.cif.gz | 9.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fye ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fye | HTTPS FTP |
-Related structure data
-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
#1: Protein | Mass: 24793.301 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PSE380 / Production host: Escherichia coli (E. coli) References: UniProt: P36936, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Chemical | ChemComp-CD / |
#3: 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: 2.38 Å3/Da / Density % sol: 48.24 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 5 mg/ml enzyme, 50mM Tris, 50mM cacodylate, 1mM CdSo4, 2-10% PEG 35000, equilibrated against a NaCl solution, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 9.5 / Method: vapor diffusion / Details: Conlin, C.A., (1994) J.Bacteriol., 176, 166. | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1 |
Detector | Type: BRANDEIS / Detector: CCD / Date: Jun 6, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→20 Å / Num. obs: 68270 / % possible obs: 93.6 % / Redundancy: 2 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.2→1.24 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.274 / Num. unique all: 5515 / % possible all: 76.1 |
Reflection | *PLUS Num. measured all: 137483 |
Reflection shell | *PLUS % possible obs: 76.1 % |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.2→10 Å / Num. parameters: 1689 / Num. restraintsaints: 2071 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: This structure was obtained by refining entry 1FY2 with SHELX and anisotropic B-factors using the same data. The authors recommend 1FY2 (isotropic B-factor refinement)as the better of the two structures.
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Refine analyze | Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1876 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.159 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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