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- PDB-1rdp: Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Gala... -

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Basic information

Entry
Database: PDB / ID: 1rdp
TitleCholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand BV3
Componentscholera toxin B protein (CTB)
KeywordsTOXIN / Bivalent / Cholera / Pentamer / Complex
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-BV3 / TRIETHYLENE GLYCOL / Cholera enterotoxin subunit B
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsPickens, J.C. / Mitchell, D.D. / Liu, J. / Tan, X. / Zhang, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E.
CitationJournal: Chem.Biol. / Year: 2004
Title: Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer.
Authors: Pickens, J.C. / Mitchell, D.D. / Liu, J. / Tan, X. / Zhang, Z. / Verlinde, C.L. / Hol, W.G. / Fan, E.
History
DepositionNov 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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

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Assembly

Deposited unit
D: cholera toxin B protein (CTB)
E: cholera toxin B protein (CTB)
F: cholera toxin B protein (CTB)
G: cholera toxin B protein (CTB)
H: cholera toxin B protein (CTB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,76112
Polymers58,1165
Non-polymers7,6457
Water8,899494
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15650 Å2
ΔGint-96 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.090, 66.079, 78.715
Angle α, β, γ (deg.)90.00, 105.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
cholera toxin B protein (CTB)


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ctxB / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P01556
#2: Chemical
ChemComp-BV3 / 1,3-BIS-([[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBU TENYL]-AMINO-ETHYL]-AMINO-CARBONYLOXY)-2-AMINO-PROPANE / BV3


Mass: 1474.482 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C63H91N15O26
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 12% PEG 8000, 50 mM NaCl, 100 mM Tris-HCl, 20mM MgCl2, and 2.3mM BV3, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2003
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 105335 / Num. obs: 100384 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.4 / Num. unique all: 6952 / % possible all: 63.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
XTALVIEWrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CHB

3chb


Resolution: 1.35→48.22 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.942 / SU ML: 0.037 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, Maximum Likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.17052 5029 5 %RANDOM
Rwork0.12986 ---
all0.13194 100384 --
obs0.13194 100384 91.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.928 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.03 Å2
2--0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 140 494 4727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224312
X-RAY DIFFRACTIONr_bond_other_d0.0010.023745
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9755840
X-RAY DIFFRACTIONr_angle_other_deg0.8673.0018773
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024634
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02762
X-RAY DIFFRACTIONr_nbd_refined0.2270.3842
X-RAY DIFFRACTIONr_nbd_other0.2970.34684
X-RAY DIFFRACTIONr_nbtor_other0.0850.52296
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5669
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3550.329
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.516
X-RAY DIFFRACTIONr_mcbond_it2.65832581
X-RAY DIFFRACTIONr_mcangle_it3.47644194
X-RAY DIFFRACTIONr_scbond_it4.37641731
X-RAY DIFFRACTIONr_scangle_it6.08361646
X-RAY DIFFRACTIONr_rigid_bond_restr2.11234312
X-RAY DIFFRACTIONr_sphericity_free21.69915494
X-RAY DIFFRACTIONr_sphericity_bonded6.002154233
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 242 -
Rwork0.208 4743 -
obs-4743 62.01 %

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