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- PDB-4fp5: Heat-labile enterotoxin ILT-IIbB5 S74A mutant -

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Basic information

Entry
Database: PDB / ID: 4fp5
TitleHeat-labile enterotoxin ILT-IIbB5 S74A mutant
ComponentsHeat-labile enterotoxin IIB, B chain
KeywordsTOXIN / B pentamer LT-IIb S74A mutant
Function / homology
Function and homology information


perturbation of signal transduction in another organism / host cell membrane / toxin activity / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #50 / Type II heat-labile enterotoxin, B subunit / Type II heat-labile enterotoxin, B subunit superfamily / Type II heat-labile enterotoxin , B subunit (LT-IIB) / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Heat-labile enterotoxin IIB, B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCody, V. / Pace, J. / Nawar, H. / Liang, S. / Connell, T. / Hajishengallis, G.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structure-activity correlations of variant forms of the B pentamer of Escherichia coli type II heat-labile enterotoxin LT-IIb with Toll-like receptor 2 binding.
Authors: Cody, V. / Pace, J. / Nawar, H.F. / King-Lyons, N. / Liang, S. / Connell, T.D. / Hajishengallis, G.
History
DepositionJun 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Heat-labile enterotoxin IIB, B chain
E: Heat-labile enterotoxin IIB, B chain
F: Heat-labile enterotoxin IIB, B chain
G: Heat-labile enterotoxin IIB, B chain
H: Heat-labile enterotoxin IIB, B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2616
Polymers53,1655
Non-polymers961
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-103 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.410, 67.585, 155.554
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
Heat-labile enterotoxin IIB, B chain / LT-IIB


Mass: 10633.076 Da / Num. of mol.: 5 / Fragment: heat-labile enterotoxin B pentamer / Mutation: S74A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: DH5aF'Kan / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P43529
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Bis-Tris propane, pH8.5, 20% PEG3350 and 200 mM KSCN, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 21, 2011 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.4→48.41 Å / Num. all: 101201 / Num. obs: 96076 / % possible obs: 98.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.029 / Net I/σ(I): 14.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.2 / Num. unique all: 14547 / Rsym value: 0.15 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q5B

1q5b


Resolution: 1.4→41.14 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 0.898 / SU ML: 0.037 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.061 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21086 5052 5 %RANDOM
Rwork0.18511 ---
all0.196 96076 --
obs0.1864 96076 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.4→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3695 0 5 409 4109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0193858
X-RAY DIFFRACTIONr_angle_refined_deg2.4471.9425238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.74224.562160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77315660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.521526
X-RAY DIFFRACTIONr_chiral_restr0.1490.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212892
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 366 -
Rwork0.231 6622 -
obs-14647 99.99 %

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