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Yorodumi- PDB-7eqz: Crystal structure of Carboxypeptidase B complexed with Potato Car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eqz | ||||||
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Title | Crystal structure of Carboxypeptidase B complexed with Potato Carboxypeptidase Inhibitor | ||||||
Components |
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Keywords | Hydrolase/Hydrolase inhibitor / ANTIVIRAL PROTEIN / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | Function and homology information carboxypeptidase B / endopeptidase inhibitor activity / metallocarboxypeptidase activity / proteolysis / zinc ion binding Similarity search - Function | ||||||
Biological species | Aedes aegypti (yellow fever mosquito) Solanum tuberosum (potato) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Choong, Y.K. / Gavor, E. / Jobichen, C. / Sivaraman, J. | ||||||
Funding support | Singapore, 1items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Structure of Aedes aegypti carboxypeptidase B1-inhibitor complex uncover the disparity between mosquito and non-mosquito insect carboxypeptidase inhibition mechanism. Authors: Gavor, E. / Choong, Y.K. / Jobichen, C. / Mok, Y.K. / Kini, R.M. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eqz.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eqz.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 7eqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eqz_validation.pdf.gz | 923.8 KB | Display | wwPDB validaton report |
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Full document | 7eqz_full_validation.pdf.gz | 924.5 KB | Display | |
Data in XML | 7eqz_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7eqz_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/7eqz ftp://data.pdbj.org/pub/pdb/validation_reports/eq/7eqz | HTTPS FTP |
-Related structure data
Related structure data | 4cpaS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32930.691 Da / Num. of mol.: 1 / Fragment: Mature region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aedes aegypti (yellow fever mosquito) / Gene: CPB-I / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q6J661, carboxypeptidase B |
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#2: Protein/peptide | Mass: 3991.495 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Solanum tuberosum (potato) / References: UniProt: P01075 |
#3: Chemical | ChemComp-ZN / |
#4: Chemical | ChemComp-GLY / |
#5: Water | ChemComp-HOH / |
Compound details | In chain I, the peptide bond between VAL I 38 and GLY I 39 was cleaved, and the free glycine was captured. |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 1.6M Ammonium sulfate, 0.1M Sodium HEPES pH 7.5, 0.1M Sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→31.89 Å / Num. obs: 15975 / % possible obs: 96.61 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.55 Å2 / Rsym value: 0.069 / Net I/σ(I): 48.29 |
Reflection shell | Resolution: 2.2→2.27 Å / Num. unique obs: 1009 / Rsym value: 0.118 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4cpa Resolution: 2.2→31.89 Å / SU ML: 0.1799 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8066 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→31.89 Å
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Refine LS restraints |
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LS refinement shell |
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