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Yorodumi- PDB-5mrv: Crystal structure of human carboxypeptidase O in complex with NvCI -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mrv | ||||||
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Title | Crystal structure of human carboxypeptidase O in complex with NvCI | ||||||
Components |
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Keywords | HYDROLASE / Digestive Metallocarboxypeptidase / food digestion / carboxypeptidase inhibitor / Brush Border enzyme | ||||||
Function / homology | Function and homology information : / metalloendopeptidase inhibitor activity / negative regulation of endopeptidase activity / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / apical plasma membrane / proteolysis / extracellular space / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Nerita versicolor (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 Å | ||||||
Authors | Garcia-Pardo, J. / Garcia-Guerrero, M.C. / Fernandez-Alvarez, R. / Lyons, P. / Aviles, F.X. / Lorenzo, J. / Reverter, D. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Crystal structure and mechanism of human carboxypeptidase O: Insights into its specific activity for acidic residues. Authors: Garcia-Guerrero, M.C. / Garcia-Pardo, J. / Berenguer, E. / Fernandez-Alvarez, R. / Barfi, G.B. / Lyons, P.J. / Aviles, F.X. / Huber, R. / Lorenzo, J. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mrv.cif.gz | 163.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mrv.ent.gz | 126.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/5mrv ftp://data.pdbj.org/pub/pdb/validation_reports/mr/5mrv | HTTPS FTP |
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-Related structure data
Related structure data | 2pcuS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 40907.863 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPO / Plasmid: pTriEx-7 vector / Cell line (production host): HEK293 F / Production host: Homo sapiens (human) References: UniProt: Q8IVL8, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases #2: Protein | | Mass: 5956.682 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Carboxypeptidase Inhibitor obtained from the marine snail Nerita versicolor Source: (gene. exp.) Nerita versicolor (invertebrata) / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P86912 #3: Chemical | #4: Sugar | ChemComp-NAG / Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Formula: C8H15NO6 / Source: (gene. exp.) Homo sapiens (human) / Gene: CPO / Plasmid: pTriEx-7 vector / Cell line (production host): HEK293 F / Production host: Homo sapiens (human) #5: 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: 2.74 Å3/Da / Density % sol: 55.08 % / Description: Monoclinic crystals C 1 2 1 |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Drops were prepared by mixing equal volumes of protein solution (CPO:NvCI molar ratio, 1:0.5) at 5 mg/ml (in 5 mM Tris-HCl pH 7.3, 100 mM NaCl, 1 mM B-mercaptoetanol) and reservoir solution ...Details: Drops were prepared by mixing equal volumes of protein solution (CPO:NvCI molar ratio, 1:0.5) at 5 mg/ml (in 5 mM Tris-HCl pH 7.3, 100 mM NaCl, 1 mM B-mercaptoetanol) and reservoir solution containning HEPES pH 7.0, 200 mM ammonium choride and 20% PEG6000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.854→64.984 Å / Num. obs: 79948 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rsym value: 0.084 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.854→1.86 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / CC1/2: 0.68 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PCU Resolution: 1.854→59.947 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.854→59.947 Å
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Refine LS restraints |
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LS refinement shell |
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