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- PDB-2cb4: Crystal structure of the catalytic domain of the mosquitocidal to... -

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Basic information

Entry
Database: PDB / ID: 2cb4
TitleCrystal structure of the catalytic domain of the mosquitocidal toxin from Bacillus sphaericus, mutant E197Q
ComponentsMOSQUITOCIDAL TOXIN
KeywordsTOXIN / 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 speciesBACILLUS SPHAERICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


Theoretical massNumber of molelcules
Total (without water)464,15214
Polymers464,15214
Non-polymers00
Water24,3201350
1
A: MOSQUITOCIDAL TOXIN
B: MOSQUITOCIDAL TOXIN
C: MOSQUITOCIDAL TOXIN
D: MOSQUITOCIDAL TOXIN
E: MOSQUITOCIDAL TOXIN
F: MOSQUITOCIDAL TOXIN
G: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)232,0767
Polymers232,0767
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
H: MOSQUITOCIDAL TOXIN
I: MOSQUITOCIDAL TOXIN
J: MOSQUITOCIDAL TOXIN
K: MOSQUITOCIDAL TOXIN
L: MOSQUITOCIDAL TOXIN
M: MOSQUITOCIDAL TOXIN
N: MOSQUITOCIDAL TOXIN


Theoretical massNumber of molelcules
Total (without water)232,0767
Polymers232,0767
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)123.710, 143.267, 135.814
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
MOSQUITOCIDAL TOXIN


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 / water


Mass: 18.015 Da / Num. of mol.: 1350 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 197 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN E, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN F, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN G, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN H, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN K, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN L, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN M, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN N, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN I, GLU 197 TO GLN ENGINEERED RESIDUE IN CHAIN J, GLU 197 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: 2.75 Å3/Da / Density % sol: 54.99 %
Crystal growpH: 4.3 / Details: 0.1 M NA ACETATE (PH 4.3), 4-10% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9798
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 2.5→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
TNT5.6.1refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 8035 5 %0.1754
Rwork0.1744 ---
all0.1754 ---
obs0.1744 160530 --
Solvent computationSolvent model: BABINET MODEL WITH MASK / Bsol: 149 Å2 / ksol: 0.89 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29330 0 0 1350 30680
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.013301561.25
X-RAY DIFFRACTIONt_angle_deg1.3409221.5
X-RAY DIFFRACTIONt_dihedral_angle_d16.4172760
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00810083
X-RAY DIFFRACTIONt_gen_planes0.01342848
X-RAY DIFFRACTIONt_it1.93015620
X-RAY DIFFRACTIONt_nbd0.0872055
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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