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- PDB-1qb5: ESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER -

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Basic information

Entry
Database: PDB / ID: 1qb5
TitleESCHERICHIA COLI HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER
ComponentsPROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)
KeywordsENTEROTOXIN
Function / homology
Function and homology information


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 / Resolution: 1.9 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: To be Published
Title: Crystal Structures of the B-Pentamer from E. coli Enterotoxin LT-IIb
Authors: Merritt, E.A. / Van den Akker, F. / Connell, T.D. / Holmes, R.K. / Hol, W.G.J.
#1: Journal: Structure / Year: 1996
Title: Crystal Structure of a New Heat-Labile Enterotoxin, LT-IIb
Authors: Van Den Akker, F. / Sarfaty, S. / Twiddy, E.M. / Connell, T.D. / Holmes, R.K. / Hol, W.G.J.
#2: Journal: J.Bacteriol. / Year: 1989
Title: Cloning, Nucleotide Sequence, and Hybridization Studies of the Type IIb Heat- Labile Enterotoxin Gene of Escherichia coli
Authors: Pickett, C.L. / Twiddy, E.M. / Coker, C. / Holmes, R.K.
History
DepositionApr 30, 1999Deposition site: RCSB / Processing site: NDB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)
E: PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)
F: PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)
G: PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)
H: PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)


Theoretical massNumber of molelcules
Total (without water)53,8915
Polymers53,8915
Non-polymers00
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-85 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.091, 67.573, 90.287
Angle α, β, γ (deg.)90.00, 113.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PROTEIN (HEAT LABILE ENTEROTOXIN TYPE IIB B-PENTAMER)


Mass: 10778.190 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: HB101 / Plasmid: BLUESCRIPT-KS VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: P43529
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.57 Å3/Da / Density % sol: 21.4 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.5 / Details: VAPOR DIFFUSION, SITTING DROP, pH 5.5

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Data collection

DiffractionMean temperature: 275 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 36737 / Num. obs: 36737 / % possible obs: 94 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 14
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 5.4 / % possible all: 92

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97refinement
RefinementResolution: 1.9→10 Å / Num. parameters: 1576 / Num. restraintsaints: 3339 / Cross valid method: FREE R / σ(F): 0
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
RfactorNum. reflection% reflectionSelection details
Rfree0.237 158 5 %RANDOM
Rwork0.177 ---
all0.177 31666 --
obs0.177 31666 94.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeOccupancy sum hydrogen: 3675 / Occupancy sum non hydrogen: 3938
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 0 188 3938
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.01
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0

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