+Open data
-Basic information
Entry | Database: PDB / ID: 1fno | ||||||
---|---|---|---|---|---|---|---|
Title | PEPTIDASE T (TRIPEPTIDASE) | ||||||
Components | PEPTIDASE T | ||||||
Keywords | HYDROLASE / metallo peptidase / protease | ||||||
Function / homology | Function and homology information tripeptide aminopeptidase / tripeptide aminopeptidase activity / peptide catabolic process / metallopeptidase activity / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å | ||||||
Authors | Hakansson, K. / Miller, C.G. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 2002 Title: Structure of Peptidase T from Salmonella typhimurium Authors: Hakansson, K. / Miller, C.G. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization of Peptidase T from Salmonella typhimurium Authors: Hakansson, K. / Broder, D. / Wang, A.H. / Miller, C.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fno.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fno.ent.gz | 69 KB | Display | PDB format |
PDBx/mmJSON format | 1fno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fno_validation.pdf.gz | 430 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fno_full_validation.pdf.gz | 443.8 KB | Display | |
Data in XML | 1fno_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1fno_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/1fno ftp://data.pdbj.org/pub/pdb/validation_reports/fn/1fno | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The biological assembly is probably a dimer constructed from chain A and a symmetry partner generated by the two-fold symmetry. |
-Components
#1: Protein | Mass: 46679.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Plasmid: PET28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834 References: UniProt: P26311, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.53 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor equilibration / pH: 7.5 Details: 10 mg/ml enzyme in 10 mM Tris pH 7.5 mixed with an equal amount and equilibrated against 50mM Tris pH 7.5, 1.2 M ammonium sulfate, vapor equilibration, temperature 293K | |||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: Hakansson, K., (2000) Acta Crystallogr., Sect.D, 56, 924. PH range low: 9 / PH range high: 7 | |||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9879 |
Detector | Type: ADSC / Detector: CCD / Date: Sep 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9879 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 20598 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 23.4 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.246 / Num. unique all: 2019 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 99755 |
Reflection shell | *PLUS % possible obs: 99.2 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.4→500 Å / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→500 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 500 Å / σ(F): 0 / Rfactor obs: 0.224 / Rfactor Rfree: 0.262 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_d / Dev ideal: 1.7 |