+Open data
-Basic information
Entry | Database: PDB / ID: 3gt4 | ||||||
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Title | Structure of proteinase K with the magic triangle I3C | ||||||
Components | proteinase K | ||||||
Keywords | HYDROLASE / PHASING TOOL / 5-AMINO-2 / 4 / 6-TRIIODOISOPHTHALIC ACID / I3C / MAGIC TRIANGLE / 6-TRIBROMOISOPHTHALIC ACID / B3C / MAD TRIANGLE / Disulfide bond / Metal-binding / Protease / Serine protease / Zymogen | ||||||
Function / homology | Function and homology information peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Engyodontium album (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å | ||||||
Authors | Beck, T. / Gruene, T. / Sheldrick, G.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: The magic triangle goes MAD: experimental phasing with a bromine derivative Authors: Beck, T. / Gruene, T. / Sheldrick, G.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: A magic triangle for experimental phasing of macromolecules Authors: Beck, T. / Krasauskas, A. / Gruene, T. / Sheldrick, G.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gt4.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gt4.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/3gt4 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/3gt4 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | Nonpolymer details | THE REFERENCE OF I3C IS ACTA CRYSTALLOGRAPHICA SECTION E(2008) E64, O1286 TITLE: 5-AMINO-2,4,6- ...THE REFERENCE OF I3C IS ACTA CRYSTALLOG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 0.1M TRIS, 1.28M ammonium sulfate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 106 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.54178 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2008 / Details: double crystal Si(111) fixed-exit monochromator |
Radiation | Monochromator: double crystal Si(111) fixed-exit monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→47.9 Å / Num. all: 22828 / Num. obs: 22828 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.14 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.76→1.86 Å / Redundancy: 1.73 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 8.3 / % possible all: 62 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: none Resolution: 1.76→47.9 Å / Num. parameters: 9560 / Num. restraintsaints: 8581 / Occupancy max: 1 / Occupancy min: 0.11 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 61.97 Å2 / Biso mean: 10.204 Å2 / Biso min: 0 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→47.9 Å
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Refine LS restraints |
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