+Open data
-Basic information
Entry | Database: PDB / ID: 2vsa | ||||||
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Title | Structure and mode of action of a mosquitocidal holotoxin | ||||||
Components | MOSQUITOCIDAL TOXIN | ||||||
Keywords | TOXIN / ADP-RIBOSYLTRANSFERASE / LECTIN / RICIN-B-LIKE DOMAIN | ||||||
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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | LYSINIBACILLUS SPHAERICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | ||||||
Authors | Treiber, N. / Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure and Mode of Action of a Mosquitocidal Holotoxin Authors: Treiber, N. / Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AL" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vsa.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vsa.ent.gz | 140.6 KB | Display | PDB format |
PDBx/mmJSON format | 2vsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vsa_validation.pdf.gz | 429.4 KB | Display | wwPDB validaton report |
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Full document | 2vsa_full_validation.pdf.gz | 448.1 KB | Display | |
Data in XML | 2vsa_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 2vsa_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vsa ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vsa | HTTPS FTP |
-Related structure data
Related structure data | 2vseC 2cb4S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 97407.227 Da / Num. of mol.: 1 / Fragment: HOLOTOXIN, RESIDUES 30-870 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LYSINIBACILLUS SPHAERICUS (bacteria) / Strain: SSII-1 / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q03988 |
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#2: Water | ChemComp-HOH / |
Sequence details | MTX 30-870 WAS USED FOR CRYSTALLIZ |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.5 % Description: FOR LECTIN DOMAINS, A MODEL WAS CALCULATED USING FFAS03 AND SCWRL |
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Crystal grow | pH: 8.5 / Details: 3% (W/V) PEG-6000 0.1 M TRIS, PH 8.5 0.1 M KCL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 |
Detector | Type: MARREASEARCH / Detector: CCD / Date: Sep 26, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 29077 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Rsym value: 0.107 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4 / Rsym value: 0.46 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CB4 Resolution: 2.89→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 30.352 / SU ML: 0.28 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 189-192 AND 262-270 ARE MISSING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.99 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→50 Å
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Refine LS restraints |
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