+Open data
-Basic information
Entry | Database: PDB / ID: 2boa | |||||||||
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Title | Human procarboxypeptidase A4. | |||||||||
Components | CARBOXYPEPTIDASE A4 | |||||||||
Keywords | HYDROLASE / METALLOPROCARBOXYPEPTIDASE / X-RAY CRYSTAL STRUCTURE / ZYMOGEN / METALLOPROTEASE / EXOPROPEPTIDASE / CARBOXYPEPTIDASE | |||||||||
Function / homology | Function and homology information hormone catabolic process / peptide catabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Garcia-Castellanos, R. / Bonet-Figueredo, R. / Pallares, I. / Ventura, S. / Aviles, F.X. / Vendrell, J. / Gomis-Ruth, F.X. | |||||||||
Citation | Journal: Cell.Mol.Life Sci. / Year: 2005 Title: Detailed Molecular Comparison between the Inhibition Mode of A/B-Type Carboxypeptidases in the Zymogen State and by the Endogenous Inhibitor Latexin. Authors: Garcia-Castellanos, R. / Bonet-Figueredo, R. / Pallares, I. / Ventura, S. / Aviles, F.X. / Vendrell, J. / Gomis-Ruth, F.X. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Structure of Human Carboxypeptidase A4 with its Endogenous Protein Inhibitor, Latexin. Authors: Pallares, I. / Bonet, R. / Garcia-Castellanos, R. / Ventura, S. / Aviles, F.X. / Vendrell, J. / Gomis-Rueth, F.X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2boa.cif.gz | 180.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2boa.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 2boa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2boa_validation.pdf.gz | 418 KB | Display | wwPDB validaton report |
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Full document | 2boa_full_validation.pdf.gz | 437.9 KB | Display | |
Data in XML | 2boa_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 2boa_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2boa ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2boa | HTTPS FTP |
-Related structure data
Related structure data | 1ayeS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45612.926 Da / Num. of mol.: 2 / Fragment: ALPHA/BETA-HYDROLASE DOMAIN, RESIDUES 18-421 Source method: isolated from a genetically manipulated source Details: N-GLYCOSYLATION AT ASN148 IN BOTH COPIES PRESENT / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9UI42 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 380 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | UNIPROT ENTRY CONTAINS ALSO THE SIGNAL SEQUENCE. DUE TO THE CLONING PROCEDURE, THE FIRST GLUTAMINE ...UNIPROT ENTRY CONTAINS ALSO THE SIGNAL SEQUENCE. DUE TO THE CLONING PROCEDURE, THE FIRST GLUTAMINE OF THE MATURE PROTEIN IS REPLACED BY ARGININE IN THE PRESENT ENTRY. IN THE PRESENT PDB ENTRY, THE RESIDUES OF THE TWO CHEMICALLY |
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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: 2.6 Å3/Da / Density % sol: 56 % |
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Crystal grow | pH: 9 / Details: 14.5% PEG4000; 0.1M BICINE PH 9.0; 0.2M MAGCL2. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→62 Å / Num. obs: 46526 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.2 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AYE Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Displacement parameters | Biso mean: 35.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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