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- PDB-1jr0: CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1jr0
TitleCHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0011
Componentscholera toxin B subunit
KeywordsTOXIN / ENTEROTOXIN / RECEPTOR / B-PENTAMER
Function / homology
Function and homology information


host cell surface binding / galactose binding / positive regulation of tyrosine phosphorylation of STAT protein / catalytic complex / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane
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
Chem-A24 / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
CitationJournal: Chem.Biol. / Year: 2002
Title: Anchor-based design of improved cholera toxin and E. coli heat-labile enterotoxin receptor binding antagonists that display multiple binding modes.
Authors: Pickens, J.C. / Merritt, E.A. / Ahn, M. / Verlinde, C.L. / Hol, W.G. / Fan, E.
History
DepositionAug 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: cholera toxin B subunit
E: cholera toxin B subunit
F: cholera toxin B subunit
G: cholera toxin B subunit
H: cholera toxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,40310
Polymers58,1165
Non-polymers2,2875
Water12,520695
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: cholera toxin B subunit
E: cholera toxin B subunit
F: cholera toxin B subunit
G: cholera toxin B subunit
H: cholera toxin B subunit
hetero molecules

D: cholera toxin B subunit
E: cholera toxin B subunit
F: cholera toxin B subunit
G: cholera toxin B subunit
H: cholera toxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,80720
Polymers116,23310
Non-polymers4,57410
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area33320 Å2
ΔGint-104 kcal/mol
Surface area38200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.098, 66.064, 78.565
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
cholera toxin B subunit


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ctxb / Production host: Escherichia coli (E. coli) / References: UniProt: P01556
#2: Chemical
ChemComp-A24 / (3-NITRO-5-(2-MORPHOLIN-4-YL-ETHYLAMINOCARBONYL)PHENYL)-GALACTOPYRANOSIDE / BMSC-0011


Mass: 457.432 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H27N3O10
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 1.83 Å3/Da / Density % sol: 43.93 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3000, NaCl, MgCl2, Tris HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16.0 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
3200 mM1dropNaCl
43 mM1dropNaN3
51 mMEDTA1drop
650 mM1reservoirNaCl
7100 mMTris-HCl1reservoirpH7.5
830 %PEG30001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 11, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.3→22 Å / Num. obs: 110275 / % possible obs: 89 % / Redundancy: 4 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.1
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4097 / % possible all: 40
Reflection
*PLUS
Highest resolution: 1.3 Å
Reflection shell
*PLUS
% possible obs: 40 %

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementStarting model: 3CHB

3chb


Resolution: 1.3→22 Å / Num. parameters: 44038 / Num. restraintsaints: 52704 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1834 5513 5 %RANDOM
obs0.1307 -100 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 4085 / Occupancy sum non hydrogen: 4925
Refinement stepCycle: LAST / Resolution: 1.3→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 160 695 4925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0366
X-RAY DIFFRACTIONs_zero_chiral_vol0.061
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.054
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.083
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 104753 / Rfactor Rwork: 0.1307
Solvent computation
*PLUS
Displacement parameters
*PLUS

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