+Open data
-Basic information
Entry | Database: PDB / ID: 1qji | ||||||
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Title | Structure of astacin with a transition-state analogue inhibitor | ||||||
Components | ASTACIN | ||||||
Keywords | HYDROLASE(METALLOPROTEINASE) / ASTACINS / METZINCINS | ||||||
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 FLUVIATILIS (noble crayfish) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å | ||||||
Authors | Grams, F. / Bode, W. / Stocker, W. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1996 Title: Structure of Astacin with a Transition-State Analogue Inhibitor Authors: Grams, F. / Dive, V. / Yiotakis, A. / Yiallouros, I. / Vassiliou, S. / Zwilling, R. / Bode, W. / Stocker, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qji.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qji.ent.gz | 52.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qji_validation.pdf.gz | 475.3 KB | Display | wwPDB validaton report |
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Full document | 1qji_full_validation.pdf.gz | 477.1 KB | Display | |
Data in XML | 1qji_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | 1qji_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/1qji ftp://data.pdbj.org/pub/pdb/validation_reports/qj/1qji | HTTPS FTP |
-Related structure data
Related structure data | 1qjjC 1astS S: Starting model for refinement C: citing same article (ref.) |
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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: 22617.977 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Source method: isolated from a natural source Details: IN COMPLEX WITH A BOUND TRANSITION-STATE ANALOGUE PHOSPHINIC PSEUDOPEPTIDE CARBOBENZOXY-PRO-LYS-PHE-Y(PO2)-ALA-PRO-OME Source: (natural) ASTACUS FLUVIATILIS (noble crayfish) / Cell: F-CELL / Organ: MIDGUT GLAND / Secretion: DIGESTIVE FLUID / References: UniProt: P07584, astacin |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PKF / |
#4: Water | ChemComp-HOH / |
Compound details | THE CDNA ENCODES TWO ADDITIONAL C-TERMINAL RESIDUES ARG-HIS THAT ARE CLEAVED OFF ...THE CDNA ENCODES TWO ADDITIONAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.26 % | ||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: HANGING DROP VAPOUR DIFFUSION PH 7.0, 1M AMMONIUM SULFATE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Gomiz-Ruth, F.-W., (1993) J. Mol. Biol., 229, 945. / pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 2.14 |
Detector | Type: BRUKER NONIUS FAST / Detector: AREA DETECTOR / Date: Jun 15, 1994 / Details: COLLIMATOR PINHOLES |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.14 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→8 Å / Num. obs: 12071 / % possible obs: 77.6 % / Observed criterion σ(I): 0.6 / Redundancy: 2.5 % / Rmerge(I) obs: 0.109 |
Reflection shell | Resolution: 2.14→2.19 Å / % possible all: 30.4 |
Reflection | *PLUS Num. measured all: 39277 |
Reflection shell | *PLUS % possible obs: 30.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AST Resolution: 2.14→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Displacement parameters | Biso mean: 27.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.14→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: 9366 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |