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- PDB-1efi: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH PARA-AMINOPHENY... -

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Basic information

Entry
Database: PDB / ID: 1efi
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH PARA-AMINOPHENYL-ALPHA-D-GALACTOPYRANOSIDE
ComponentsPROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
KeywordsTOXIN / ENTEROTOXIN
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
Similarity search - Function
Heat-labile enterotoxin, B chain / Heat-labile enterotoxin beta chain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-aminophenyl alpha-D-galactopyranoside / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Exploration of the GM1 receptor-binding site of heat-labile enterotoxin and cholera toxin by phenyl-ring-containing galactose derivatives.
Authors: Fan, E. / Merritt, E.A. / Zhang, Z. / Pickens, J.C. / Roach, C. / Ahn, M. / Hol, W.G.
#1: Journal: Structure / Year: 1997
Title: Structural Foundation for the Design of Receptor Antagonists Targeting Escherichia Heat-Labile Enterotoxin
Authors: Merritt, E.A. / Sarfaty, S. / Feil, I.K. / Hol, W.G.
#2: Journal: Mol.Microbiol. / Year: 1994
Title: Galactose-Binding Site in Escherichia Coli Heat-Labile Enterotoxin (LT) and Cholera Toxin (CT)
Authors: Merritt, E.A. / Sixma, T.K. / Kalk, K.H. / van Zanten, B.A. / Hol, W.G.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Escherichia Coli Heat-Labile Enterotoxin, a Close Relative of Cholera Toxin
Authors: Sixma, T.K. / Kalk, K.H. / van Zanten, B.A. / Dauter, Z. / Kingma, J. / Witholt, B. / Hol, W.G.
History
DepositionFeb 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
E: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
F: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
G: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
H: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,39410
Polymers59,0385
Non-polymers1,3565
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14960 Å2
ΔGint-39 kcal/mol
Surface area21100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 96.340, 63.580
Angle α, β, γ (deg.)90.00, 107.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN) / LT-I


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Plasmid: PROFIT / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Sugar
ChemComp-GAT / 4-aminophenyl alpha-D-galactopyranoside / P-AMINOPHENYL-ALPHA-D-GALACTOPYRANOSIDE


Type: D-saccharide / Mass: 271.266 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H17NO6
IdentifierTypeProgram
p-aminophenyl-a-D-galactopyranosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6 / Details: pH 5.6, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMsodium citrate/HCl1reservoir
222 %(w/v)PEG350 MME1reservoir
32.5 mg/mlprotein1drop
410 mMHEPES1drop
52.5 mMp-aminophenyl-alpha-D-galactopyranoside1drop

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Data collection

DiffractionMean temperature: 100 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: 1.6→25 Å / Num. all: 50240 / Num. obs: 50240 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 3.76
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.055 / Num. unique all: 3479
Reflection
*PLUS
% possible obs: 78 %
Reflection shell
*PLUS
% possible obs: 54 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLOR3.851refinement
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.6→25 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2034 4 %RANDOM
Rwork0.188 ---
obs0.188 50230 77.9 %-
Displacement parametersBiso mean: 12 Å2
Baniso -1Baniso -2Baniso -3
1-5.6126 Å20 Å2-2.0485 Å2
2---3.3045 Å20 Å2
3----2.3082 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 95 695 4910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.56
X-RAY DIFFRACTIONx_dihedral_angle_d24.09
X-RAY DIFFRACTIONx_improper_angle_d1.51
LS refinement shellResolution: 1.6→1.63 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2321 47 3.2 %
Rwork0.2017 1119 -
obs--47 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM1.CHOLOCALLY MODIFIED TOPH1.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.09
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.51
LS refinement shell
*PLUS
% reflection Rfree: 3.2 %

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