+Open data
-Basic information
Entry | Database: PDB / ID: 3i78 | ||||||
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Title | 35/99/170/186/220-loops of FXa in SGT | ||||||
Components | Trypsin | ||||||
Keywords | HYDROLASE / BETA SHEETS / SERINE PROTEASE / Disulfide bond / Protease / Zymogen | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces griseus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Page, M.J. / Di Cera, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Combinatorial Enzyme Design Probes Allostery and Cooperativity in the Trypsin Fold. Authors: Page, M.J. / Di Cera, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i78.cif.gz | 57.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i78.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 3i78.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i78_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 3i78_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 3i78_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 3i78_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i7/3i78 ftp://data.pdbj.org/pub/pdb/validation_reports/i7/3i78 | HTTPS FTP |
-Related structure data
Related structure data | 3i77C 3beuS C: citing same article (ref.) S: Starting model for refinement |
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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: 24197.061 Da / Num. of mol.: 1 Mutation: 27 substitutions in the 35, 99, 170, 186 and 220-loops Source method: isolated from a genetically manipulated source Details: 35/99/170/186/220-loops of FXa in SGT / Source: (gene. exp.) Streptomyces griseus (bacteria) / Gene: sprT / Plasmid: pWB980 / Production host: Bacillus subtilis (bacteria) / Strain (production host): WB700 / References: UniProt: P00775, trypsin | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-BEN / | ||
#4: Chemical | ChemComp-SO4 / Sequence details | 27 SUBSTITUTI | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.69 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2.0 M Ammonium sulfate, 0.1 M CAPS, 75 mM NaCl, 25 mM Benzamidine, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 10, 2009 |
Radiation | Monochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→36 Å / Num. all: 7874 / Num. obs: 7515 / % possible obs: 97.58 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 56.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3BEU Resolution: 3→35.94 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.847 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 18.784 / SU ML: 0.339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.078 / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.16 Å2 / Biso mean: 56.984 Å2 / Biso min: 38.75 Å2
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Refinement step | Cycle: LAST / Resolution: 3→35.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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