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- PDB-2cb6: Crystal structure of the catalytic domain of the mosquitocidal to... -

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Basic information

Entry
Database: PDB / ID: 2cb6
TitleCrystal structure of the catalytic domain of the mosquitocidal toxin from Bacillus sphaericus, mutant E195Q
ComponentsMOSQUITOCIDAL TOXIN
KeywordsTOXIN / ADP-RIBOSYLTRANSFERASE
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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsReinert, D.J. / Carpusca, I. / Aktories, K. / Schulz, G.E.
CitationJournal: 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
DepositionDec 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOSQUITOCIDAL TOXIN
B: MOSQUITOCIDAL TOXIN
C: MOSQUITOCIDAL TOXIN
D: MOSQUITOCIDAL TOXIN
E: MOSQUITOCIDAL TOXIN
F: MOSQUITOCIDAL TOXIN
G: MOSQUITOCIDAL TOXIN
H: MOSQUITOCIDAL TOXIN
I: MOSQUITOCIDAL TOXIN
J: MOSQUITOCIDAL TOXIN
K: MOSQUITOCIDAL TOXIN
L: MOSQUITOCIDAL TOXIN
M: MOSQUITOCIDAL TOXIN
N: MOSQUITOCIDAL TOXIN
O: MOSQUITOCIDAL TOXIN
P: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)526,70816
Polymers526,70816
Non-polymers00
Water00
1
A: MOSQUITOCIDAL TOXIN
B: MOSQUITOCIDAL TOXIN
C: MOSQUITOCIDAL TOXIN
D: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)131,6774
Polymers131,6774
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: MOSQUITOCIDAL TOXIN
F: MOSQUITOCIDAL TOXIN
G: MOSQUITOCIDAL TOXIN
H: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)131,6774
Polymers131,6774
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
I: MOSQUITOCIDAL TOXIN
J: MOSQUITOCIDAL TOXIN
K: MOSQUITOCIDAL TOXIN
L: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)131,6774
Polymers131,6774
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
M: MOSQUITOCIDAL TOXIN
N: MOSQUITOCIDAL TOXIN
O: MOSQUITOCIDAL TOXIN
P: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)131,6774
Polymers131,6774
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.302, 175.802, 335.503
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MOSQUITOCIDAL TOXIN


Mass: 32919.254 Da / Num. of mol.: 16 / 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
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 195 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN E, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN F, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN G, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN H, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN I, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN J, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN K, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN L, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN M, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN N, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN O, GLU 195 TO GLN ENGINEERED RESIDUE IN CHAIN P, GLU 195 TO GLN

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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: 3.59 Å3/Da / Density % sol: 65.45 %
Crystal growpH: 6.3
Details: 100 MM NA-K PHOSPHATE (PH 6.3), 8-14% (W/V) PEG 8000, 50-150 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9787
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 126014 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 53 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CB4

2cb4


Resolution: 3→50 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 6301 5 %0.2281
Rwork0.2271 ---
all0.2281 ---
obs0.2271 126013 --
Solvent computationSolvent model: BABINET MODEL WITH MASK / Bsol: 187 Å2 / ksol: 1 e/Å3
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31202 0 0 0 31202
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.008320911
X-RAY DIFFRACTIONt_angle_deg1.167435321
X-RAY DIFFRACTIONt_dihedral_angle_d17.606182810
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00810422
X-RAY DIFFRACTIONt_gen_planes0.0145735
X-RAY DIFFRACTIONt_it0.9943209120
X-RAY DIFFRACTIONt_nbd0.0736905
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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