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Yorodumi- PDB-4a94: Structure of the carboxypeptidase inhibitor from Nerita versicolo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4a94 | ||||||
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Title | Structure of the carboxypeptidase inhibitor from Nerita versicolor in complex with human CPA4 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CPA4 / NVCI / PCI / LCI | ||||||
Function / homology | Function and homology information metalloendopeptidase inhibitor activity / hormone catabolic process / negative regulation of endopeptidase activity / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / 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: 1.7 Å | ||||||
Authors | Covaleda, G. / Alonso, M. / Chavez, M.A. / Aviles, F.X. / Reverter, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Crystal Structure of a Novel Metallo-Carboxypeptidase Inhibitor from the Marine Mollusk Nerita Versicolor in Complex with Human Carboxypeptidase A4. Authors: Covaleda, G. / Alonso Del Rivero, M. / Chavez, M.A. / Aviles, F.X. / Reverter, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4a94.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4a94.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 4a94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4a94_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 4a94_full_validation.pdf.gz | 460.4 KB | Display | |
Data in XML | 4a94_validation.xml.gz | 28.8 KB | Display | |
Data in CIF | 4a94_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/4a94 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a94 | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 34851.031 Da / Num. of mol.: 2 / Fragment: RESIDUES 112-421 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: KOMAGATAELLA PASTORIS (fungus) References: UniProt: Q9UI42, Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases #2: Protein | Mass: 5956.682 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NERITA VERSICOLOR (invertebrata) / Production host: KOMAGATAELLA PASTORIS (fungus) / References: UniProt: P86912*PLUS #3: Chemical | #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→48.33 Å / Num. obs: 79658 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.7→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 98.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.093 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.83 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.369 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.7→46.093 Å
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Refine LS restraints |
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LS refinement shell |
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