+Open data
-Basic information
Entry | Database: PDB / ID: 4kts | ||||||
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Title | Bovine trypsin in complex with microviridin J at pH 8.5 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Serine protease / Hydrolase / Natural product inhibitor / Protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Microcystis aeruginosa MRC (bacteria) Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Quitterer, F. / Groll, M. / Hertweck, C. / Dittmann, E. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2014 Title: Harnessing the evolvability of tricyclic microviridins to dissect protease-inhibitor interactions. Authors: Weiz, A.R. / Ishida, K. / Quitterer, F. / Meyer, S. / Kehr, J.C. / Muller, K.M. / Groll, M. / Hertweck, C. / Dittmann, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kts.cif.gz | 118.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kts.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kts.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kts_validation.pdf.gz | 433.6 KB | Display | wwPDB validaton report |
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Full document | 4kts_full_validation.pdf.gz | 433.9 KB | Display | |
Data in XML | 4kts_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 4kts_validation.cif.gz | 22.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/4kts ftp://data.pdbj.org/pub/pdb/validation_reports/kt/4kts | HTTPS FTP |
-Related structure data
Related structure data | 4ktuC 3mywS 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: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreatic trypsin; chain A / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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#2: Protein/peptide | Type: Cyclic peptide / Class: Enzyme inhibitor / Mass: 1724.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microcystis aeruginosa MRC (bacteria) / Gene: mdnA / Production host: Escherichia coli (E. coli) / References: UniProt: B2G3C8, Microviridin J |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-PEG / |
#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: 2.63 Å3/Da / Density % sol: 53.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris, 0.2 M lithium sulfate, 25% PEG 3350 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→30 Å / Num. all: 65619 / Num. obs: 65291 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.3→1.4 Å / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 4.6 / % possible all: 99.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MYW Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.952 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.505 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→15 Å
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Refine LS restraints |
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