+Open data
-Basic information
Entry | Database: PDB / ID: 5xx3 | ||||||
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Title | A BPTI-[5,55] variant with C14GA38G mutations | ||||||
Components | Pancreatic trypsin inhibitor | ||||||
Keywords | HYDROLASE / HYDROLASE INHIBITOR | ||||||
Function / homology | Function and homology information trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / 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 / potassium channel inhibitor activity / negative regulation of platelet aggregation / 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: 1.12 Å | ||||||
Authors | Islam, M.M. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Hydrophobic surface residues can stabilize a protein through improved water-protein interactions. Authors: Islam, M.M. / Kobayashi, K. / Kidokoro, S.I. / Kuroda, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xx3.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xx3.ent.gz | 53.1 KB | Display | PDB format |
PDBx/mmJSON format | 5xx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/5xx3 ftp://data.pdbj.org/pub/pdb/validation_reports/xx/5xx3 | HTTPS FTP |
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-Related structure data
Related structure data | 5xx2C 5xx4C 5xx5C 2zvxS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 6353.217 Da / Num. of mol.: 2 / Mutation: A14G, A38G 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 | ChemComp-SO4 / #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: 2.14 Å3/Da / Density % sol: 42.55 % / Description: two chains in the asymmetric unit |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000; 0.2M Lithium Sulfate; 0.1M Tris-HCl, pH8.5 |
-Data collection
Diffraction | Mean temperature: 101 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 28, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→53.87 Å / Num. obs: 44641 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 4.32 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5.04 / Rsym value: 0.328 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZVX Resolution: 1.12→53.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.05 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / 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: 10.819 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→53.87 Å
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Refine LS restraints |
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