+Open data
-Basic information
Entry | Database: PDB / ID: 1yme | ||||||
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Title | STRUCTURE OF CARBOXYPEPTIDASE | ||||||
Components | CARBOXYPEPTIDASE A ALPHA | ||||||
Keywords | CARBOXYPEPTIDASE / METALLOPROTEINASE / METALLOEXOPROTEINASE | ||||||
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 / Resolution: 1.53 Å | ||||||
Authors | Greenblatt, H.M. / Tucker, P.A. / Shoham, G. | ||||||
Citation | 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yme.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yme.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yme_validation.pdf.gz | 416.4 KB | Display | wwPDB validaton report |
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Full document | 1yme_full_validation.pdf.gz | 426.1 KB | Display | |
Data in XML | 1yme_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 1yme_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/1yme ftp://data.pdbj.org/pub/pdb/validation_reports/ym/1yme | HTTPS FTP |
-Related 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 / Source method: isolated from a natural source / Details: METALLOENZYME (ZN) / Source: (natural) Bos taurus (cattle) / Organ: PANCREAS / References: UniProt: P00730, carboxypeptidase A |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.19 % | ||||||||||||||||||
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Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: microdialysisDetails: Shoham, G., (1984) Proc. Natl. Acad. Sci. USA., 81, 7767. | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: 1991 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 34352 / % possible obs: 79 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.036 |
Reflection | *PLUS Highest resolution: 1.53 Å / Num. measured all: 58534 |
-Processing
Software |
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Refinement | Resolution: 1.53→5 Å / σ(F): 2 Details: PROLSQ, AND TNT DEFAULT FINAL RMS COORD. SHIFT 0.013 ANGSTROMS
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Displacement parameters | Biso mean: 18.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→5 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.148 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |