+Open data
-Basic information
Entry | Database: PDB / ID: 1fy4 | ||||||
---|---|---|---|---|---|---|---|
Title | FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION | ||||||
Components |
| ||||||
Keywords | HYDROLASE / beta barrel | ||||||
Function / homology | Function and homology information trypsin / serine-type endopeptidase activity / proteolysis / extracellular region Similarity search - Function | ||||||
Biological species | Fusarium oxysporum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.81 Å | ||||||
Authors | Rypniewski, W.R. / Oestergaard, P. / Noerregaard-Madsen, M. / Dauter, M. / Wilson, K.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding. Authors: Rypniewski, W.R. / Ostergaard, P.R. / Norregaard-Madsen, M. / Dauter, M. / Wilson, K.S. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1995 Title: Structure of inhibited trypsin from Fusarium oxysporum at 1.55A Authors: Rypniewski, W.R. / Dambmann, C. / von der Osten, C. / Dauter, M. / Wilson, K.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fy4.cif.gz | 149.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fy4.ent.gz | 126.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fy4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fy4_validation.pdf.gz | 445.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1fy4_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 1fy4_validation.xml.gz | 18.1 KB | Display | |
Data in CIF | 1fy4_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fy4 ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fy4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 22200.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Fusarium oxysporum (fungus) / References: UniProt: P35049, trypsin | ||
---|---|---|---|
#2: Protein/peptide | Mass: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Chemical | ChemComp-SO4 / | ||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: sodium sulphate, sodium citrate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 0.8468 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8468 Å / Relative weight: 1 |
Reflection | Resolution: 0.81→20 Å / Num. all: 1184962 / Num. obs: 1184962 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 3.1 |
Reflection shell | Resolution: 0.81→0.82 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.0269 / Num. unique all: 7566 / % possible all: 88.4 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 159467 / Num. measured all: 1184962 |
Reflection shell | *PLUS % possible obs: 88.4 % |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 0.81→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: least-squares refinement against I's. Full-matrix least-squares at the end to obtain error estimates
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.81→20 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / Rfactor all: 0.108 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.132 |