+Open data
-Basic information
Entry | Database: PDB / ID: 1k9o | |||||||||
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Title | CRYSTAL STRUCTURE OF MICHAELIS SERPIN-TRYPSIN COMPLEX | |||||||||
Components |
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Keywords | Hydrolase/Hydrolase Inhibitor / Michaelis serpin-protease complex inhibitory triad / Hydrolase-Hydrolase Inhibitor COMPLEX | |||||||||
Function / homology | Function and homology information Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsin / Neutrophil degranulation / digestion / collagen catabolic process / response to nutrient / response to bacterium / serine-type endopeptidase inhibitor activity ...Antimicrobial peptides / Alpha-defensins / Activation of Matrix Metalloproteinases / trypsin / Neutrophil degranulation / digestion / collagen catabolic process / response to nutrient / response to bacterium / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Manduca sexta (tobacco hornworm) Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Ye, S. / Cech, A.L. / Belmares, R. / Bergstrom, R.C. / Tong, Y. / Corey, D.R. / Kanost, M.R. / Goldsmith, E.J. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: The structure of a Michaelis serpin-protease complex. Authors: Ye, S. / Cech, A.L. / Belmares, R. / Bergstrom, R.C. / Tong, Y. / Corey, D.R. / Kanost, M.R. / Goldsmith, E.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1k9o.cif.gz | 132.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k9o.ent.gz | 101.2 KB | Display | PDB format |
PDBx/mmJSON format | 1k9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k9o_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 1k9o_full_validation.pdf.gz | 451.8 KB | Display | |
Data in XML | 1k9o_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 1k9o_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/1k9o ftp://data.pdbj.org/pub/pdb/validation_reports/k9/1k9o | HTTPS FTP |
-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: 42016.988 Da / Num. of mol.: 1 / Mutation: A353K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Plasmid: H6PQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P14754 |
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#2: Protein | Mass: 23798.838 Da / Num. of mol.: 1 / Mutation: S195A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PYT / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00763, trypsin |
#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: 2.67 Å3/Da / Density % sol: 53.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 3350, DTT, POTASSIUM PHOSPHATE, SODIUM PHOSPHATE, 2-PROPANOL, AMMONIUM CHLORIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS PH range low: 6.5 / PH range high: 6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å |
Detector | Detector: CCD / Date: Dec 10, 1999 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. obs: 30999 / % possible obs: 98.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 1.76 / Num. unique all: 30999 / % possible all: 95.6 |
Reflection | *PLUS Num. measured all: 186342 |
Reflection shell | *PLUS % possible obs: 95.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1SEK AND 1DPO Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.158 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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