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- PDB-5jb4: A simplified BPTI variant containing 21 alanines out 58 of residues -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jb4 | ||||||
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Title | A simplified BPTI variant containing 21 alanines out 58 of residues | ||||||
![]() | Pancreatic trypsin inhibitor | ||||||
![]() | HYDROLASE INHIBITOR / Bovine pancreatic trypsin inhibitor variant / sequence simplification / 21 alanines / protein design | ||||||
Function / homology | ![]() trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Islam, M.M. | ||||||
![]() | ![]() Title: Crystal structures of highly simplified BPTIs provide insights into hydration-driven increase of unfolding enthalpy Authors: Islam, M.M. / Yohda, M. / Kidokoro, S. / Kuroda, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.1 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 446.3 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 17 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jb5C ![]() 5jb6C ![]() 5jb7C ![]() 3aubS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 5842.605 Da / Num. of mol.: 3 / Mutation: C49G,C73V,M87L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 4000, LITHIUM SULFATE, TRIS-HCL |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. obs: 17360 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 3.16 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.16 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AUB Resolution: 1.99→39.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.878 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.154 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→39.81 Å
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Refine LS restraints |
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