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- PDB-1llr: CHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0012 -

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Basic information

Entry
Database: PDB / ID: 1llr
TitleCHOLERA TOXIN B-PENTAMER WITH LIGAND BMSC-0012
ComponentsCHOLERA TOXIN B SUBUNIT
KeywordsTOXIN / ENTEROTOXIN / RECEPTOR / B-PENTAMER
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
Chem-FNG / Chem-LNQ / : / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.46 Å
AuthorsMerritt, E.A. / Hol, W.G.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Characterization and crystal structure of a high-affinity pentavalent receptor-binding inhibitor for cholera toxin and E. coli heat-labile enterotoxin.
Authors: Merritt, E.A. / Zhang, Z. / Pickens, J.C. / Ahn, M. / Hol, W.G. / Fan, E.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 600HETEROGEN Ligand BMS-0012 is a pentavalent ligand consisting of a pentacyclen core to which are ...HETEROGEN Ligand BMS-0012 is a pentavalent ligand consisting of a pentacyclen core to which are linked five long arms, each containing two 'linker' moities and terminating in a 'finger' derived from metanitrophenylgalactoside. For refinement the ligand was broken into pieces: FNG (for 'finger') is derived from metanitrophenyl-alpha-D-galactopyranoside. LNQ (for 'linker') is a linker group present in two copies per arm, only one of which is included in the model. There is an additional pentane-2-one which links the LNQ to the core. COR (for 'core', 1,4,7,10,13pentaaza-cyclopentadecane) is not present in this PDB file because it was not sufficiently well ordered to be included in the structural model. The central core of the ligand is inferred to lie near the central pore of the pentameric protein. Water numbering retained from 3CHB except that canonical sites (formerly 7000) are given the following numbers: 001-009 canonical waters at binding site of chain D 101-109 canonical waters at binding site of chain E 201-209 canonical waters at binding site of chain F 301-309 canonical waters at binding site of chain G 401-409 canonical waters at binding site of chain H All other waters (formerly 9000) given residue numbers 1001-1733.
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED
Remark 700SHEET DETERMINATION METHOD: AUTHOR PROVIDED

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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)61,33915
Polymers58,1165
Non-polymers3,22310
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17850 Å2
ΔGint-34 kcal/mol
Surface area20340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.391, 65.964, 78.146
Angle α, β, γ (deg.)90.00, 105.97, 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: GenBank: 48890, UniProt: Q57193*PLUS
#2: Sugar
ChemComp-FNG / 5-aminocarbonyl-3-nitrophenyl alpha-D-galactopyranoside


Type: D-saccharide / Mass: 344.274 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H16N2O9
IdentifierTypeProgram
5-aminocarbonyl-3-nitrophenyl-a-D-galactopyranoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-LNQ / 3-AMINO-4-{3-[2-(2-PROPOXY-ETHOXY)-ETHOXY]-PROPYLAMINO}-CYCLOBUT-3-ENE-1,2-DIONE


Mass: 300.351 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H24N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 300, NACL, MGCL2, TRIS HCL, pH 7.50, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.0 mg/mlprotein1drop
2100 mMTris-HCl1droppH7.5
30.17 mM71drop
450 mM1reservoirNaCl
5100 mMTris-HCl1reservoirpH7.5
642 %PEG3001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. all: 84902 / Num. obs: 84902 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.6
Reflection shellResolution: 1.46→1.51 Å / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2 / % possible all: 81
Reflection
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 50 Å / % possible obs: 97 % / Redundancy: 4 %
Reflection shell
*PLUS
% possible obs: 82 % / Num. unique obs: 7083 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC4refinement
RefinementResolution: 1.46→27 Å / Cor.coef. Fo:Fc: 0.96029 / Cor.coef. Fo:Fc free: 0.94911 / SU B: 1.17719 / SU ML: 0.04407 / SU R Cruickshank DPI: 0.0805 / SU Rfree: 0.07012 / Cross valid method: RFREE / ESU R: 0.08 / ESU R Free: 0.07
Details: Protein + FNG residues refined with anisotropic Uij. Remainder of ligand atoms in model refined with isotropic U.
RfactorNum. reflectionSelection details
Rfree0.19072 4244 RANDOM
Rwork0.14869 --
obs0.14869 84750 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: Babinet model plus mask
Refinement stepCycle: LAST / Resolution: 1.46→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 225 570 4893
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.061
X-RAY DIFFRACTIONp_mcangle_it1.61.5
X-RAY DIFFRACTIONp_scbond_it2.482
X-RAY DIFFRACTIONp_scangle_it3.443
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.160.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
1.46-1.5320.2575350.1729643X-RAY DIFFRACTION20
1.532-1.6130.2245290.1299717X-RAY DIFFRACTION20
1.613-1.7010.2044570.1059092X-RAY DIFFRACTION20
1.701-1.8010.1863980.0948139X-RAY DIFFRACTION20
1.801-1.9120.183720.0897213X-RAY DIFFRACTION20
1.912-2.0380.1593220.0946417X-RAY DIFFRACTION20
2.038-2.1830.1673250.0985592X-RAY DIFFRACTION20
2.183-2.3490.1562680.1034840X-RAY DIFFRACTION20
2.349-2.5420.1682080.1054200X-RAY DIFFRACTION20
2.542-2.770.1611920.1213549X-RAY DIFFRACTION20
2.77-3.0430.1781390.1412982X-RAY DIFFRACTION20
3.043-3.3760.1731320.1572454X-RAY DIFFRACTION20
3.376-3.7910.1611140.1691975X-RAY DIFFRACTION20
3.791-4.3210.172790.2091540X-RAY DIFFRACTION20
4.321-5.0250.192650.2361150X-RAY DIFFRACTION20
5.025-6.0020.358410.325865X-RAY DIFFRACTION20
6.002-7.450.412380.407573X-RAY DIFFRACTION20
7.45-9.8210.428250.53330X-RAY DIFFRACTION20
9.821-14.4030.74840.538170X-RAY DIFFRACTION20
14.403-270.78310.80165X-RAY DIFFRACTION20
Refinement
*PLUS
Highest resolution: 1.46 Å / Lowest resolution: 27 Å / Rfactor Rfree: 0.191 / Rfactor Rwork: 0.149
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d0.039

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