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Yorodumi- PDB-3qw8: Crystal structure of the protease domain of Botulinum Neurotoxin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qw8 | ||||||
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Title | Crystal structure of the protease domain of Botulinum Neurotoxin Serotype A with a peptide inhibitor CRGC | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / endopeptidase / syntaxin / bio-warfare agent / membrane / metal-binding / metalloprotease / protease / secreted / transmembrane / SNAP25 / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane Similarity search - Function | ||||||
Biological species | Clostridium botulinum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.6 Å | ||||||
Authors | Kumaran, D. / Swaminathan, S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Peptide inhibitors of botulinum neurotoxin serotype A: design, inhibition, cocrystal structures, structure-activity relationship and pharmacophore modeling. Authors: Kumar, G. / Kumaran, D. / Ahmed, S.A. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qw8.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qw8.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 3qw8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qw/3qw8 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/3qw8 | HTTPS FTP |
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-Related structure data
Related structure data | 3qw5C 3qw6C 3qw7C 3bwiS 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 49415.727 Da / Num. of mol.: 1 / Fragment: light chain (UNP residues 1-424) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Strain: Hall / ATCC 3502 / NCTC 13319 / Type A / Gene: botA, CBO0806, CLC_0862 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: A5HZZ9, UniProt: P0DPI1*PLUS, bontoxilysin |
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#2: Protein/peptide | Mass: 436.554 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 5 types, 337 molecules
#3: Chemical | ChemComp-ZN / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-EDO / | #7: 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: 2.16 Å3/Da / Density % sol: 43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 22% PEG3350, 0.3 M ammonium sulfate, pH 6.80, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 13, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 51397 / Num. obs: 51397 / % possible obs: 91.5 % / Observed criterion σ(F): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2885 / % possible all: 62.3 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER Starting model: PDB ENTRY 3BWI Resolution: 1.6→29.44 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 90076.44 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5743 Å2 / ksol: 0.369954 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.44 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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