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Yorodumi- PDB-2cb4: Crystal structure of the catalytic domain of the mosquitocidal to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cb4 | ||||||
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Title | Crystal structure of the catalytic domain of the mosquitocidal toxin from Bacillus sphaericus, mutant E197Q | ||||||
Components | MOSQUITOCIDAL TOXIN | ||||||
Keywords | TOXIN / ADP-RIBOSYLTRANSFERASE | ||||||
Function / homology | Function and homology information Clostridium botulinum HA-17 domain / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Ricin-type beta-trefoil lectin domain-like / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | BACILLUS SPHAERICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structure of the Mosquitocidal Toxin from Bacillus Sphaericus. Authors: Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cb4.cif.gz | 737.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cb4.ent.gz | 620.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cb4_validation.pdf.gz | 539 KB | Display | wwPDB validaton report |
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Full document | 2cb4_full_validation.pdf.gz | 593.2 KB | Display | |
Data in XML | 2cb4_validation.xml.gz | 137.2 KB | Display | |
Data in CIF | 2cb4_validation.cif.gz | 175.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/2cb4 ftp://data.pdbj.org/pub/pdb/validation_reports/cb/2cb4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 33153.723 Da / Num. of mol.: 14 / Fragment: CATALYTIC DOMAIN RESIDUES 30-308 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS SPHAERICUS (bacteria) / Strain: SSII-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q03988 #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 197 TO GLN ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 54.99 % |
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Crystal grow | pH: 4.3 / Details: 0.1 M NA ACETATE (PH 4.3), 4-10% (W/V) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 316595 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.5→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.5→50 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO
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Solvent computation | Solvent model: BABINET MODEL WITH MASK / Bsol: 149 Å2 / ksol: 0.89 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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