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Yorodumi- PDB-3huv: Carboxypeptidase A liganded to an organic small-molecule: conform... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3huv | ||||||
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Title | Carboxypeptidase A liganded to an organic small-molecule: conformational changes | ||||||
Components | Carboxypeptidase A1 (Pancreatic) | ||||||
Keywords | HYDROLASE / CPA / M14 protease / metallocarboxypeptidase / Carboxypeptidase | ||||||
Function / homology | Function and homology information carboxypeptidase A / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fernandez, D. / Boix, E. / Aviles, F.X. / Vendrell, J. | ||||||
Citation | Journal: To be Published Title: Carboxypeptidase A liganded to an organic small-molecule: conformational changes Authors: Fernandez, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3huv.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3huv.ent.gz | 56.5 KB | Display | PDB format |
PDBx/mmJSON format | 3huv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3huv_validation.pdf.gz | 419.3 KB | Display | wwPDB validaton report |
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Full document | 3huv_full_validation.pdf.gz | 422 KB | Display | |
Data in XML | 3huv_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 3huv_validation.cif.gz | 21.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/3huv ftp://data.pdbj.org/pub/pdb/validation_reports/hu/3huv | HTTPS FTP |
-Related structure data
Related structure data | 2ctbS 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: 34721.750 Da / Num. of mol.: 1 / Fragment: UNP residues 111-419 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: CPA1 / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): KM71 / References: UniProt: A6H6Y4 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.26 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% PEG8000, 0.02M tris, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 29, 2007 |
Radiation | Monochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8148 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→55.815 Å / Num. all: 21281 / Num. obs: 21263 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 16.03 Å2 / Rmerge(I) obs: 0.164 / Rsym value: 0.136 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3091 / Rsym value: 0.49 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CTB Resolution: 1.9→21 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.731 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.175 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TYR248 RESIDUE IS RELATED TO CPA CATALYTIC MECHANISM. VERY WEAK ELECTRON DENSITY FOR TYR248 SIDE CHAIN WAS FOUND. SIDE CHAIN ATOMS WERE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TYR248 RESIDUE IS RELATED TO CPA CATALYTIC MECHANISM. VERY WEAK ELECTRON DENSITY FOR TYR248 SIDE CHAIN WAS FOUND. SIDE CHAIN ATOMS WERE MODELLED FROM THE SECOND MOST POPULATED ROTAMER FROM THE REFINEMENT PROGRAM WITH THE PHENOLIC HYDROXYL GROUP POINTING TOWARDS THE SOLVENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.045 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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