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- PDB-1ee3: Cadmium-substituted bovine pancreatic carboxypeptidase A (alfa-fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ee3 | ||||||
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Title | Cadmium-substituted bovine pancreatic carboxypeptidase A (alfa-form) at pH 7.5 and 2 mM chloride in monoclinic crystal form | ||||||
![]() | PROTEIN (CARBOXYPEPTIDASE A) | ||||||
![]() | HYDROLASE / ALFA/BETA FOLD | ||||||
Function / homology | ![]() carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jensen, F. / Bukrinsky, T. / Bjerrum, J. / Larsen, S. | ||||||
![]() | ![]() 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: ![]() Title: Native Carboxypeptidase A in a New Crystal Environment Reveals A Different Conformation of the Important Tyrosine 248 Authors: Bukrinsky, J.T. / Bjerrum, M.T. / Kadziola, A. #2: ![]() Title: Carboxypeptidase A: Native, Zinc-Removed and Mercury-Replaced Forms Authors: Greenblatt, H.M. / Feinberg, H. / Tucker, P.A. / Shoham, G. #3: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 79.9 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.4 KB | Display | ![]() |
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Full document | ![]() | 428.7 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ellC ![]() 1elmC ![]() 5cpaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 291 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 15, 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: 1.7→40 Å / Num. obs: 31210 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 29 |
Reflection shell | Resolution: 1.69→1.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5.4 / % possible all: 84.9 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Num. measured all: 348864 |
Reflection shell | *PLUS % possible obs: 84.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CPA.PDB Resolution: 1.7→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: 33.7 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.72 Å / Total num. of bins used: 31
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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 Rfactor Rfree: 0.1978 / Rfactor Rwork: 0.1737 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.0055 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS % reflection Rfree: 5 % |