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- PDB-1eef: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH BOUND LIGAND PEPG -

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Basic information

Entry
Database: PDB / ID: 1eef
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH BOUND LIGAND PEPG
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
alpha-D-galactopyranose / 2-PHENETHYL-2,3-DIHYDRO-PHTHALAZINE-1,4-DIONE / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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.
History
DepositionJan 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 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_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)
L: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
M: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
N: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
O: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
P: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,94224
Polymers118,07510
Non-polymers2,86714
Water19,5101083
1
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)60,47112
Polymers59,0385
Non-polymers1,4337
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-53 kcal/mol
Surface area20220 Å2
MethodPISA
2
L: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
M: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
N: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
O: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
P: PROTEIN (HEAT-LABILE ENTEROTOXIN B CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,47112
Polymers59,0385
Non-polymers1,4337
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15750 Å2
ΔGint-48 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.540, 65.020, 101.930
Angle α, β, γ (deg.)90.00, 115.47, 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.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINEPig / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P32890
#2: Sugar
ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE / Galactose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-I06 / 2-PHENETHYL-2,3-DIHYDRO-PHTHALAZINE-1,4-DIONE


Mass: 266.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14N2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1083 / 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: 2.2 Å3/Da / Density % sol: 45.16 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
12.5 mg/mlprotein1drop
210 mMHEPES1drop
4100 mMcacodylate1reservoir
5200 mM1reservoirMgCl2
635 %2-propanol1reservoir
3PEPG1drop0.001ml

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 20, 1998 / Details: DOUBLY-FOCUSED MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22 Å / Num. all: 97336 / Num. obs: 97336 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.35 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.4
Reflection shellResolution: 1.82→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.115 / % possible all: 99.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED LTB B-PENTAMER STRUCTURE

Resolution: 1.8→22 Å / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4889 5 %RANDOM
Rwork0.182 ---
all0.182 97336 --
obs0.182 96986 99.6 %-
Displacement parametersBiso mean: 16 Å2
Baniso -1Baniso -2Baniso -3
1-3.5288 Å20 Å2-0.0087 Å2
2---1.218 Å20 Å2
3----2.3108 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 200 1083 9523
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.568
X-RAY DIFFRACTIONx_dihedral_angle_d23.7
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_mcbond_it2.32
X-RAY DIFFRACTIONx_mcangle_it3.64
X-RAY DIFFRACTIONx_scbond_it2.32
X-RAY DIFFRACTIONx_scangle_it3.64
LS refinement shellResolution: 1.82→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.213 177 -
Rwork0.23 3591 -
obs--99.9 %
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
Highest resolution: 1.8 Å / Lowest resolution: 22 Å / σ(F): 1 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.213 / Rfactor Rwork: 0.23

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