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Open data
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Basic information
Entry | Database: PDB / ID: 1ds3 | ||||||
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Title | CRYSTAL STRUCTURE OF OMTKY3-CH2-ASP19I | ||||||
![]() | OVOMUCOID | ||||||
![]() | HYDROLASE INHIBITOR / canonical protein inhibitor / ovomucoid / reduced peptide bond / OMTKY3 | ||||||
Function / homology | ![]() molecular function inhibitor activity / serine-type endopeptidase inhibitor activity / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Bateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N.G. | ||||||
![]() | ![]() Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with ...Title: Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I Authors: Bateman, K.S. / Huang, K. / Anderson, S. / Lu, W. / Qasim, M.A. / Laskowski Jr., M. / James, M.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 18.1 KB | Display | ![]() |
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PDB format | ![]() | 12.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 402.3 KB | Display | ![]() |
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Full document | ![]() | 402.6 KB | Display | |
Data in XML | ![]() | 4.7 KB | Display | |
Data in CIF | ![]() | 5.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 5557.278 Da / Num. of mol.: 1 / Fragment: THIRD DOMAIN (OMTKY3) / Mutation: REDUCED PEPTIDE BOND BETWEEN LEU18I(2LU)-ASP19I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: THE PEPTIDE BOND BETWEEN LEU18I(2LU) AND ASP19I HAS BEEN REDUCED. Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 37.02 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: ammonium sulphate, no buffer, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | |||||||||||||||
Crystal grow | *PLUS Details: used seeding | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Apr 18, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→20 Å / Num. obs: 16933 / % possible obs: 92.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 10.64 |
Reflection shell | Resolution: 1.65→1.68 Å / Rmerge(I) obs: 0.245 / % possible all: 47.6 |
Reflection | *PLUS Num. obs: 4800 / Num. measured all: 16933 |
Reflection shell | *PLUS % possible obs: 47.6 % |
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Processing
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Refinement | Resolution: 1.65→20 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 | ||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.011 |