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Yorodumi- PDB-5jb4: A simplified BPTI variant containing 21 alanines out 58 of residues -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jb4 | ||||||
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Title | A simplified BPTI variant containing 21 alanines out 58 of residues | ||||||
Components | Pancreatic trypsin inhibitor | ||||||
Keywords | HYDROLASE INHIBITOR / Bovine pancreatic trypsin inhibitor variant / sequence simplification / 21 alanines / protein design | ||||||
Function / homology | Function and homology information 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 | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Islam, M.M. | ||||||
Citation | Journal: Sci Rep / Year: 2017 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jb4.cif.gz | 51.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jb4.ent.gz | 35.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jb4_validation.pdf.gz | 446.3 KB | Display | wwPDB validaton report |
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Full document | 5jb4_full_validation.pdf.gz | 446.3 KB | Display | |
Data in XML | 5jb4_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5jb4_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/5jb4 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/5jb4 | HTTPS FTP |
-Related structure data
Related structure data | 5jb5C 5jb6C 5jb7C 3aubS 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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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.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00974 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-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: 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: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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