+Open data
-Basic information
Entry | Database: PDB / ID: 1gdq | ||||||
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Title | FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION | ||||||
Components |
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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: 0.93 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 | 1gdq.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gdq.ent.gz | 110.2 KB | Display | PDB format |
PDBx/mmJSON format | 1gdq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/1gdq ftp://data.pdbj.org/pub/pdb/validation_reports/gd/1gdq | HTTPS FTP |
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-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: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
#3: Chemical | #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: 1.95 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 19K | ||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 23, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 0.93→12 Å / Num. all: 576525 / Num. obs: 576525 / % possible obs: 92.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 6 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19 |
Reflection shell | Resolution: 0.93→0.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.247 / Num. unique all: 5033 / % possible all: 86.3 |
Reflection | *PLUS Lowest resolution: 12 Å / Num. obs: 107781 / Num. measured all: 576525 |
Reflection shell | *PLUS % possible obs: 86.3 % |
-Processing
Software |
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Refinement | Resolution: 0.93→12 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: 0.93→12 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_chiral_restr / Dev ideal: 0.112 |