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Yorodumi- PDB-1qua: CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qua | ||||||
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Title | CRYSTAL STRUCTURE OF ACUTOLYSIN-C, A HEMORRHAGIC TOXIN FROM THE SNAKE VENOM OF AGKISTRODON ACUTUS, AT 2.2 A RESOLUTION | ||||||
Components | ACUTOLYSIN-C | ||||||
Keywords | TOXIN / METALLOPROTEASE / HEMORRHAGIC TOXIN / SNAKE VENOM PROTEINASE / AGKISTRODON ACUTUS | ||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / calcium ion binding / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Deinagkistrodon acutus (Chinese moccasin) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Niu, L. / Teng, M. / Zhu, X. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Structure of acutolysin-C, a haemorrhagic toxin from the venom of Agkistrodon acutus, providing further evidence for the mechanism of the pH-dependent proteolytic reaction of zinc metalloproteinases. Authors: Zhu, X. / Teng, M. / Niu, L. #1: Journal: CHIN.SCI.BULL. / Year: 1996 Title: Preliminary X-Ray Diffraction Analysis of Hemorrhagin III from the Snake Venom of Agkistrodon Acutus Authors: Gong, W. / Zhu, Z. / Niu, L. / Teng, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qua.cif.gz | 51.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qua.ent.gz | 36.3 KB | Display | PDB format |
PDBx/mmJSON format | 1qua.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qua_validation.pdf.gz | 362.5 KB | Display | wwPDB validaton report |
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Full document | 1qua_full_validation.pdf.gz | 366.3 KB | Display | |
Data in XML | 1qua_validation.xml.gz | 5.7 KB | Display | |
Data in CIF | 1qua_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/1qua ftp://data.pdbj.org/pub/pdb/validation_reports/qu/1qua | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21457.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deinagkistrodon acutus (Chinese moccasin) / Secretion: VENOM / References: UniProt: Q9W7S2, UniProt: P60244*PLUS |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.25 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
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: 2.2→20 Å / Num. obs: 10704 / % possible obs: 90.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08 |
Reflection shell | Resolution: 2.2→2.25 Å / Rmerge(I) obs: 0.263 / % possible all: 95.5 |
Reflection shell | *PLUS % possible obs: 95.5 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CRYSTAL STRUCTURE OF H2-PROTEINASE Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 22.84 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |