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- PDB-1eei: CHOLERA TOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL-ALPHA-D-G... -

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Basic information

Entry
Database: PDB / ID: 1eei
TitleCHOLERA TOXIN B-PENTAMER COMPLEXED WITH METANITROPHENYL-ALPHA-D-GALACTOSE
ComponentsPROTEIN (CHOLERA TOXIN B)
KeywordsTOXIN / ENTEROTOXIN
Function / homology
Function and homology information


extracellular region / metal ion binding
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
3-nitrophenyl alpha-D-galactopyranoside / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMEN / Resolution: 2 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: J.Mol.Biol. / Year: 1998
Title: The 1.25 A Resolution Refinement of the Cholera Toxin B-Pentamer: Evidence of Peptide Backbone Strain at the Receptor-binding Site.
Authors: Merritt, E.A. / Kuhn, P. / Sarfaty, S. / Erbe, J.L. / Holmes, R.K. / Hol, W.G.
#2: 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.J.
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_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
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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: PROTEIN (CHOLERA TOXIN B)
E: PROTEIN (CHOLERA TOXIN B)
F: PROTEIN (CHOLERA TOXIN B)
G: PROTEIN (CHOLERA TOXIN B)
H: PROTEIN (CHOLERA TOXIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,62310
Polymers58,1165
Non-polymers1,5065
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-37 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.900, 69.550, 130.660
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 (CHOLERA TOXIN B)


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: RECEPTOR BINDING SITE ON EACH MONOMER OCCUPIED BY METANITROPHENYL-ALPHA-D-GALACTOSIDE
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OGAWA 41 (CLASSICAL BIOTYPE) / Production host: Escherichia coli (E. coli) / References: UniProt: Q57193
#2: Sugar
ChemComp-GAA / 3-nitrophenyl alpha-D-galactopyranoside / METANITROPHENYL-ALPHA-D-GALACTOSIDE / 3-nitrophenyl alpha-D-galactoside / 3-nitrophenyl D-galactoside / 3-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C12H15NO8
IdentifierTypeProgram
metanitrophenyl-a-D-galactosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / 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: 2.56 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: SITTING DROP, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMTris1drop
22 mMpepstatin1drop
32 mMPMSF1drop
45 mMdithiothreitol1drop
51 mMEDTA1drop
630 mMm-nitrophenyl-alpha-D-galactopyranoside1drop
7100 mMsodium phosphate/citrate1reservoir
819 %1,2-propanediol1reservoir

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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: Apr 10, 1998 / Details: DOUBLE-FOCUS MIRRORS MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 40887 / Num. obs: 40887 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3785 / % possible all: 88
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMEN
Starting model: PDB ENTRY 3CHB

3chb


Resolution: 2→20 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1982 -RANDOM
Rwork0.2001 ---
obs0.2001 40342 100 %-
all-40362 --
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 105 455 4630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.58
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_torsion_deg24
X-RAY DIFFRACTIONx_torsion_impr_deg1.5
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 1
Solvent computation
*PLUS
Displacement parameters
*PLUS

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