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Yorodumi- PDB-1xvm: Trypsin from Fusarium oxysporum- room temperature to atomic resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xvm | ||||||
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Title | Trypsin from Fusarium oxysporum- room temperature to atomic resolution | ||||||
Components |
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Keywords | HYDROLASE / atomic resolution / mobility / room temperature | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.1 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 | 1xvm.cif.gz | 128.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xvm.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 1xvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/1xvm ftp://data.pdbj.org/pub/pdb/validation_reports/xv/1xvm | HTTPS FTP |
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-Related structure data
Related structure data | 1xvoC 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: Protein/peptide | Mass: 303.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. |
#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: 2 Å3/Da / Density % sol: 38.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: ammonium sulfate, sodium citrate, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.803 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 2, 2003 / Details: mirrors |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.1 Å / Num. all: 65556 / Num. obs: 65556 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 9 Å2 / Rsym value: 0.094 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.1→1.11 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2271 / Rsym value: 0.361 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PQ5 Resolution: 1.1→10 Å / Num. parameters: 15420 / Num. restraintsaints: 19268 / 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: 15.1 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 1475.2 / Occupancy sum non hydrogen: 1696.6 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→10 Å
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Refine LS restraints |
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