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Yorodumi- PDB-1ell: CADMIUM-SUBSTITUTED BOVINE PANCREATIC CARBOXYPEPTIDASE A (ALFA-FO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ell | ||||||
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Title | CADMIUM-SUBSTITUTED BOVINE PANCREATIC CARBOXYPEPTIDASE A (ALFA-FORM) AT PH 7.5 AND 0.25 M CHLORIDE IN MONOCLINIC CRYSTAL FORM. | ||||||
Components | CARBOXYPEPTIDASE A | ||||||
Keywords | HYDROLASE / ALFA/BETA FOLD | ||||||
Function / homology | Function and homology information carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Jensen, F. / Bukrinsky, T. / Bjerrum, J. / Larsen, S. | ||||||
Citation | Journal: J.BIOL.INORG.CHEM. / Year: 2002 Title: Three high-resolution crystal structures of cadmium-substituted carboxypeptidase A provide insight into the enzymatic function Authors: Jensen, F. / Bukrinsky, T. / Bjerrum, J. / Larsen, S. #1: Journal: Biochemistry / Year: 1998 Title: Native Carboxypeptidase a in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine 248 Authors: Bukrinsky, J.T. / Bjerrum, M.J. / Kadziola, A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Carboxypeptidase A: Native, Zinc-Removed and Mercury-Replaced Forms Authors: Greenblatt, H.M. / Feinberg, H. / Tucker, P.A. / Shoham, G. #3: Journal: Biochemistry / Year: 1997 Title: Structure and Dynamics of the Metal Site of Cadmium-Substituted Carboxypeptidase a in Solution and Crystalline States and Under Steady-State Peptide Hydrolysis Authors: Bauer, R. / Danielsen, E. / Hemmingsen, L. / Soerensen, M.V. / Ulstrup, J. / Friis, E.P. / Auld, D.S. / Bjerrum, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ell.cif.gz | 79.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ell.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ell.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ell_validation.pdf.gz | 429.9 KB | Display | wwPDB validaton report |
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Full document | 1ell_full_validation.pdf.gz | 431.3 KB | Display | |
Data in XML | 1ell_validation.xml.gz | 15.1 KB | Display | |
Data in CIF | 1ell_validation.cif.gz | 22 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/1ell ftp://data.pdbj.org/pub/pdb/validation_reports/el/1ell | HTTPS FTP |
-Related structure data
Related structure data | 1ee3C 1elmC 5cpaS C: citing same article (ref.) 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: ALFA-FORM / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A | ||
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#2: Chemical | ChemComp-CD / #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: 2.12 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microdialysis / pH: 7.5 Details: Lithium Chloride, Tris-HNO3, Cadmium Chloride, pH 7.5, MICRODIALYSIS, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 288 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 18, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→40 Å / Num. obs: 27577 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 8.1 / % possible all: 79.7 |
Reflection | *PLUS Highest resolution: 1.76 Å / Lowest resolution: 40 Å / Num. obs: 233641 / % possible obs: 97.2 % |
Reflection shell | *PLUS % possible obs: 79.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CPA Resolution: 1.76→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: MAXIMUM LIKELIHOOD MINIMIZATION OF THE STRUCTURE FACTOR AMPLITUDE DIFFERENCES.
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Solvent computation | Solvent model: CNS MASK / Bsol: 30.87 Å2 / ksol: 0.323 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.78 Å / Total num. of bins used: 27
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.1781 / Rfactor Rwork: 0.167 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0056 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Lowest resolution: 1.79 Å |