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Yorodumi- PDB-1iab: CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERT... -
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-Basic information
Entry | Database: PDB / ID: 1iab | ||||||
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Title | CRYSTAL STRUCTURES, SPECTROSCOPIC FEATURES, AND CATALYTIC PROPERTIES OF COBALT(II), COPPER(II), NICKEL(II), AND MERCURY(II) DERIVATIVES OF THE ZINC ENDOPEPTIDASE ASTACIN. A CORRELATION OF STRUCTURE AND PROTEOLYTIC ACTIVITY | ||||||
Components | ASTACIN | ||||||
Keywords | ZINC ENDOPEPTIDASE | ||||||
Function / homology | Function and homology information astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / metalloendopeptidase activity / peptidase activity ...astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / positive regulation of protein processing / fertilization / metalloendopeptidase activity / peptidase activity / cell adhesion / proteolysis / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Astacus astacus (noble crayfish) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.79 Å | ||||||
Authors | Gomis-Rueth, F.-X. / Stoecker, W. / Bode, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1994 Title: Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of ...Title: Crystal structures, spectroscopic features, and catalytic properties of cobalt(II), copper(II), nickel(II), and mercury(II) derivatives of the zinc endopeptidase astacin. A correlation of structure and proteolytic activity. Authors: Gomis-Ruth, F.X. / Grams, F. / Yiallouros, I. / Nar, H. / Kusthardt, U. / Zwilling, R. / Bode, W. / Stocker, W. #1: Journal: FEBS Lett. / Year: 1993 Title: Astacins, Serralysins, Snake Venom and Matrix Metalloproteinases Exhibit Identical Zinc-Binding Environments (Hexxhxxgxxh and met-Turn) and Topologies and Should be Grouped Into a Common Family, the 'Metzincins' Authors: Bode, W. / Gomis-Rueth, F.-X. / Stoecker, W. #2: Journal: Nature / Year: 1992 Title: Structure of Astacin and Implications for Activation of Astacins and Zinc-Ligation of Collagenases Authors: Bode, W. / Gomis-Rueth, F.X. / Huber, R. / Zwilling, R. / Stoecker, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1iab.cif.gz | 52.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iab.ent.gz | 40.7 KB | Display | PDB format |
PDBx/mmJSON format | 1iab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1iab ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1iab | HTTPS FTP |
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-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: 22617.977 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Astacus astacus (noble crayfish) / References: UniProt: P07584, astacin |
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#2: Chemical | ChemComp-CO / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging dropDetails: taken from Gomis-Ruth(1993). J. Mol. Biol., 229, 945-968. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.79 Å / Lowest resolution: 20.28 Å / Num. obs: 15568 / Num. measured all: 24671 / Rmerge(I) obs: 0.0575 |
Reflection shell | *PLUS Highest resolution: 1.83 Å / Lowest resolution: 1.91 Å / % possible obs: 38.4 % |
-Processing
Software |
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Refinement | Resolution: 1.79→8 Å / Rfactor Rwork: 0.158 / Rfactor obs: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 15334 / Rfactor obs: 0.158 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.386 |