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Yorodumi- PDB-1iac: REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-... -
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-Basic information
Entry | Database: PDB / ID: 1iac | ||||||
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Title | REFINED 1.8 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF ASTACIN, A ZINC-ENDOPEPTIDASE FROM THE CRAYFISH ASTACUS ASTACUS L. STRUCTURE DETERMINATION, REFINEMENT, MOLECULAR STRUCTURE AND COMPARISON WITH THERMOLYSIN | ||||||
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: 2.1 Å | ||||||
Authors | Gomis-Rueth, F.-X. / Stoecker, W. / Bode, W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1993 Title: Refined 1.8 A X-ray crystal structure of astacin, a zinc-endopeptidase from the crayfish Astacus astacus L. Structure determination, refinement, molecular structure and comparison with thermolysin. Authors: Gomis-Ruth, F.X. / Stocker, W. / Huber, R. / Zwilling, R. / Bode, W. #1: 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-Rueth, F.-X. / Grams, F. / Yiallouros, I. / Nar, H. / Kuesthardt, U. / Zwilling, R. / Bode, W. / Stoecker, W. #2: 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. #3: 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 | 1iac.cif.gz | 55.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1iac.ent.gz | 39.9 KB | Display | PDB format |
PDBx/mmJSON format | 1iac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/1iac ftp://data.pdbj.org/pub/pdb/validation_reports/ia/1iac | 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-HG / |
#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: 48.99 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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 Num. obs: 10213 / % possible obs: 98.57 % / Num. measured all: 27702 / Rmerge(I) obs: 0.0847 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.13 Å / % possible obs: 46.5 % |
-Processing
Software |
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Refinement | Resolution: 2.1→10 Å / Rfactor Rwork: 0.16 / Rfactor obs: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 10039 / Rfactor obs: 0.16 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 2.271 |