+Open data
-Basic information
Entry | Database: PDB / ID: 2vse | ||||||
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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: 2.5 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 SHEETS PRESENTED AS "AP", "BH" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BK" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-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 | 2vse.cif.gz | 353.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vse.ent.gz | 282 KB | Display | PDB format |
PDBx/mmJSON format | 2vse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vse_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 2vse_full_validation.pdf.gz | 504 KB | Display | |
Data in XML | 2vse_validation.xml.gz | 63.5 KB | Display | |
Data in CIF | 2vse_validation.cif.gz | 91.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/2vse ftp://data.pdbj.org/pub/pdb/validation_reports/vs/2vse | HTTPS FTP |
-Related structure data
Related structure data | 2vsaC 2cb4S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 2 / Auth seq-ID: 31 - 866 / Label seq-ID: 2 - 837
NCS oper: (Code: given Matrix: (0.51287, 0.85821, -0.02107), Vector: |
-Components
#1: Protein | Mass: 97407.227 Da / Num. of mol.: 2 / 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 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | MTX 30-870 WAS USED FOR CRYSTALLIZ | |
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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: 3.4 Å3/Da / Density % sol: 63.9 % Description: MODEL FOR RICIN B-TYPE DOMAINS WAS CALCULATED WITH FFAS03 AND SCWRL SERVERS |
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Crystal grow | pH: 8.3 Details: 0.1 M TRIS, PH 8.3 3% (W/V) PEG-6000 250 MM KCL 4% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 |
Detector | Type: MARREASEARCH / Detector: CCD / Date: Jul 12, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→75 Å / Num. obs: 87586 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.09 / Rsym value: 0.084 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.48 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CB4 Resolution: 2.5→74.54 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.62 / SU ML: 0.183 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 49.23 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→74.54 Å
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Refine LS restraints |
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