+Open data
-Basic information
Entry | Database: PDB / ID: 1xvo | ||||||
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Title | Trypsin from Fusarium oxysporum at pH 6 | ||||||
Components | trypsin | ||||||
Keywords | HYDROLASE / trypsin / atomic resolution | ||||||
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: 0.84 Å | ||||||
Authors | Schmidt, A. / Lamzin, V.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Extraction of functional motion in trypsin crystal structures. Authors: Schmidt, A. / Lamzin, V.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xvo.cif.gz | 146.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvo.ent.gz | 114 KB | Display | PDB format |
PDBx/mmJSON format | 1xvo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvo ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvo | HTTPS FTP |
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-Related structure data
Related structure data | 1xvmC 1pq5S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: Chemical | ChemComp-SO4 / #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: 1.98 Å3/Da / Density % sol: 37.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: sodium sulfate, sodium citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8126 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 5, 2004 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8126 Å / Relative weight: 1 |
Reflection | Resolution: 0.84→36 Å / Num. all: 142228 / Num. obs: 142228 / % possible obs: 91.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 4.6 Å2 / Rsym value: 0.046 / Net I/σ(I): 11 |
Reflection shell | Resolution: 0.84→0.85 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 2231 / Rsym value: 0.25 / % possible all: 57 |
-Processing
Software |
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Refinement | Starting model: 1PQ5 Resolution: 0.84→25 Å / Num. parameters: 19263 / Num. restraintsaints: 22595 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER Details: ANISOTROPIC REFINEMENT, hydrogens included, refinement against diffraction intensities
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Displacement parameters | Biso mean: 6.2 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 1502.5 / Occupancy sum non hydrogen: 2058 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.84→25 Å
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Refine LS restraints |
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