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

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Basic information

Entry
Database: PDB / ID: 1qcb
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 / Resolution: 2.2 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 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Jul 28, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.6Oct 30, 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
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-89 kcal/mol
Surface area18860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 69.000, 155.000
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
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.: 151 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 8 / Details: VAPOR DIFFUSION, SITTING DROP, pH 8.0

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 22778 / % possible obs: 83 % / Observed criterion σ(F): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.066
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.207 / % possible all: 29

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Processing

Software
NameVersionClassification
X-GENdata scaling
MACROdata reduction
AMoREphasing
X-PLOR3.851refinement
X-GENdata reduction
MACROdata scaling
RefinementResolution: 2.2→20 Å / Data cutoff low absF: 0.1 / Cross valid method: FREE R / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER / Details: BULK SOLVENT MODELING. METHOD USED : BABINET
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1540 -RANDOM
Rwork0.193 ---
all-22778 --
obs-19532 86 %-
Solvent computationSolvent model: BABINET
Displacement parametersBiso mean: 35 Å2
Baniso -1Baniso -2Baniso -3
1-4.7041 Å20 Å20 Å2
2---3.206 Å20 Å2
3----0.4009 Å2
Refine analyzeOccupancy sum non hydrogen: 3938
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3750 0 0 151 3901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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