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- PDB-1djr: HEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH M-CARBOXYPHENYL... -

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Basic information

Entry
Database: PDB / ID: 1djr
TitleHEAT-LABILE ENTEROTOXIN B-PENTAMER COMPLEXED WITH M-CARBOXYPHENYL-ALPHA-D-GALACTOSE
ComponentsHEAT-LABILE ENTEROTOXIN
KeywordsTOXIN / AB5 TOXINS / CELL RECOGNITION / SIX-STRANDED ANTIPARALLEL BETA-SHEET
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
BENZOIC ACID / alpha-D-galactopyranose / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMinke, W.E. / Pickens, J. / Merritt, E.A. / Fan, E. / Verlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Structure of m-carboxyphenyl-alpha-D-galactopyranoside complexed to heat-labile enterotoxin at 1.3 A resolution: surprising variations in ligand-binding modes.
Authors: Minke, W.E. / Pickens, J. / Merritt, E.A. / Fan, E. / Verlinde, C.L. / Hol, W.G.
History
DepositionDec 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
D: HEAT-LABILE ENTEROTOXIN
E: HEAT-LABILE ENTEROTOXIN
F: HEAT-LABILE ENTEROTOXIN
G: HEAT-LABILE ENTEROTOXIN
H: HEAT-LABILE ENTEROTOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,58116
Polymers59,0385
Non-polymers1,54311
Water14,538807
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16120 Å2
ΔGint-33 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.368, 95.040, 67.507
Angle α, β, γ (deg.)90.00, 100.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HEAT-LABILE ENTEROTOXIN / LT


Mass: 11807.539 Da / Num. of mol.: 5 / Fragment: B PENTAMER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: PORCINE / Description: PORCINE ESCHERICHIA COLI, PLASMID EWD299 / 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


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 5 / Source method: obtained synthetically / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 807 / Source method: isolated from a natural source / Formula: H2O
Compound detailsdifferent binding modes for the ligand in the five binding sites

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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: 46 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7.5
Details: PEG 6000, NaCl, Tris-HCl, pH 7.5, LIQUID DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: three-layer capillary method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
142 %PEG600011
2100 mMTris-HCl11
3200 mMMCPG12
4100 mMTris-HCl12
53.6 mg/mlprotein13
6200 mM13NaCl
71 mMEDTA13
83 mMazide13
950 mMTris-HCl13

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 1999 / Details: mirror
RadiationMonochromator: SI311 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 127782 / Num. obs: 127782 / % possible obs: 99.4 % / Redundancy: 2.9 % / Biso Wilson estimate: 9.382 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 14.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.2 / Num. unique all: 12229 / % possible all: 95.5
Reflection
*PLUS
Num. measured all: 837038
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LT5

1lt5


Resolution: 1.3→20 Å / Num. parameters: 45729 / Num. restraintsaints: 54312 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflectionSelection details
Rfree0.189 6479 RANDOM
Rwork0.134 --
all0.137 127740 -
obs0.137 127740 -
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1975)201-228
Refine analyzeNum. disordered residues: 20 / Occupancy sum hydrogen: 4171 / Occupancy sum non hydrogen: 5018
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4106 0 105 807 5018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.1
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.02
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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