+Open data
-Basic information
Entry | Database: PDB / ID: 1gdn | ||||||
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Title | FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE SUBSTRATE / beta barrel / HYDROLASE / HYDROLASE-HYDROLASE SUBSTRATE COMPLEX | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gdn.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gdn.ent.gz | 121.8 KB | Display | PDB format |
PDBx/mmJSON format | 1gdn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gdn_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 1gdn_full_validation.pdf.gz | 452.6 KB | Display | |
Data in XML | 1gdn_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 1gdn_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/1gdn ftp://data.pdbj.org/pub/pdb/validation_reports/gd/1gdn | 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
#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 | ||
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#2: Protein/peptide | Mass: 275.325 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 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.64 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 Details: sodium sulphate, sodium citrate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8468 |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 2, 1996 |
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: 700099 / Num. obs: 700099 / % possible obs: 90.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 7 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 1.8 |
Reflection shell | Resolution: 0.81→0.82 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.267 / Num. unique all: 7019 / % possible all: 81.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 156398 / Num. measured all: 700099 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 81.9 % |
-Processing
Software |
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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
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Refinement step | Cycle: LAST / Resolution: 0.81→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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