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- PDB-2vsa: Structure and mode of action of a mosquitocidal holotoxin -

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Basic information

Entry
Database: PDB / ID: 2vsa
TitleStructure and mode of action of a mosquitocidal holotoxin
ComponentsMOSQUITOCIDAL TOXIN
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE / LECTIN / RICIN-B-LIKE DOMAIN
Function / homology
Function and homology information


: / Scabin-like / 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 ...: / Scabin-like / 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 speciesLYSINIBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsTreiber, N. / Reinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E.
CitationJournal: 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
DepositionApr 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)97,4071
Polymers97,4071
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.974, 129.974, 68.816
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-2106-

HOH

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Components

#1: Protein MOSQUITOCIDAL TOXIN / MTX HOLOTOXIN


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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMTX 30-870 WAS USED FOR CRYSTALLIZATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.5 %
Description: FOR LECTIN DOMAINS, A MODEL WAS CALCULATED USING FFAS03 AND SCWRL
Crystal growpH: 8.5 / Details: 3% (W/V) PEG-6000 0.1 M TRIS, PH 8.5 0.1 M KCL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918
DetectorType: MARREASEARCH / Detector: CCD / Date: Sep 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CB4

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
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1398 5.1 %RANDOM
Rwork0.187 ---
obs0.189 26064 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 58.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20.07 Å20 Å2
2--0.15 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.89→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6737 0 0 110 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.391.9159393
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6755819
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40825.323387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.182151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9271531
X-RAY DIFFRACTIONr_chiral_restr0.1010.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025429
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.23384
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.24684
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2590
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3930.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4911.54166
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.85626669
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.22833136
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8994.52724
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.96 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.358 90
Rwork0.262 1913
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.99192.9576-0.37487.741-0.29183.5337-0.43160.5408-0.4859-0.66940.1727-0.02540.387-0.31080.2588-0.0759-0.24730.0625-0.2218-0.1878-0.042146.4591-12.54689.0596
26.46953.19380.414510.53163.38557.68560.1333-0.390.68640.184-0.41841.3524-0.3143-0.70450.28510.1018-0.32010.0747-0.2709-0.16810.409621.2502-32.78626.2995
36.77692.8341-1.09528.46121.35174.91770.5816-0.7054-0.18671.3708-0.81140.51060.0246-0.16780.22980.4029-0.48470.0847-0.0462-0.0456-0.001739.8023-9.634940.9198
47.32492.5226-1.47885.8708-2.17988.09660.8381-1.0402-0.07441.359-0.815-0.2032-0.70440.6112-0.02310.1131-0.3172-0.0654-0.27040.0057-0.358862.127914.02832.9304
52.24060.9656-0.36645.4495-1.74435.2526-0.02850.3115-0.33-0.45960.0626-0.30440.57390.214-0.034-0.34660.0195-0.0017-0.4892-0.0919-0.396167.461119.33422.938
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 294
2X-RAY DIFFRACTION2A295 - 441
3X-RAY DIFFRACTION3A442 - 582
4X-RAY DIFFRACTION4A583 - 724
5X-RAY DIFFRACTION5A725 - 866

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