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- PDB-1pzk: Cholera Toxin B-Pentamer Complexed With N-Acyl Phenyl Galactoside 9h -

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Basic information

Entry
Database: PDB / ID: 1pzk
TitleCholera Toxin B-Pentamer Complexed With N-Acyl Phenyl Galactoside 9h
ComponentsCholera Toxin B Subunit
KeywordsTOXIN / PENTAMER / MONOVALENT / INHIBITOR / CHOLERA
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-J12 / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMitchell, D.D. / Pickens, J.C. / Korotkov, K. / Fan, E. / Hol, W.G.J.
CitationJournal: Bioorg.Med.Chem. / Year: 2004
Title: 3,5-Substituted phenyl galactosides as leads in designing effective cholera toxin antagonists; synthesis and crystallographic studies
Authors: Mitchell, D.D. / Pickens, J.C. / Korotkov, K. / Fan, E. / Hol, W.G.J.
History
DepositionJul 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Aug 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 1.5Nov 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: 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)61,22510
Polymers58,1165
Non-polymers3,1095
Water11,349630
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15500 Å2
ΔGint-43 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.048, 66.137, 78.185
Angle α, β, γ (deg.)90.00, 105.78, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Cholera Toxin B Subunit / CTB / cholera toxin B protein / cholera toxin subunit B


Mass: 11623.267 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: CAA41591 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q57193
#2: Chemical
ChemComp-J12 / N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE


Mass: 621.745 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C29H43N5O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 1.87 Å3/Da / Density % sol: 33.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 36% PEG 550 MME, 50 mM NaCl, 100 mM Tris pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
136 %PEG550 MME1reservoir
250 mM1reservoirNaCl
3100 mMTris-HCl1reservoirpH7.3
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97945 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 17, 2002
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. all: 104310 / Num. obs: 104310 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.14 % / Biso Wilson estimate: 13.578 Å2 / Rsym value: 0.054 / Net I/σ(I): 22.1
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 1.86 / Num. unique all: 7413 / Rsym value: 0.402 / % possible all: 68.4
Reflection
*PLUS
Num. measured all: 342770 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 68.4 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
TRUNCATEdata reduction
XTALVIEWrefinement
HKL-2000data collection
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHB

3chb


Resolution: 1.35→33.52 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.888 / SU ML: 0.035 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.054 / ESU R Free: 0.054 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17347 5202 5 %RANDOM
Rwork0.13185 ---
all0.13389 104310 --
obs0.13389 99104 95.39 %-
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: 8.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.05 Å2
2--0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 121 630 4846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214312
X-RAY DIFFRACTIONr_bond_other_d0.0010.023809
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.9725841
X-RAY DIFFRACTIONr_angle_other_deg1.38138964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9245510
X-RAY DIFFRACTIONr_chiral_restr0.1120.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024596
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02773
X-RAY DIFFRACTIONr_nbd_refined0.2270.3845
X-RAY DIFFRACTIONr_nbd_other0.2760.34505
X-RAY DIFFRACTIONr_nbtor_other0.1040.52217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.5807
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3530.327
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.532
X-RAY DIFFRACTIONr_mcbond_it2.33832577
X-RAY DIFFRACTIONr_mcangle_it3.11744190
X-RAY DIFFRACTIONr_scbond_it4.20941725
X-RAY DIFFRACTIONr_scangle_it5.69461626
X-RAY DIFFRACTIONr_rigid_bond_restr1.61824302
X-RAY DIFFRACTIONr_sphericity_free16.12310630
X-RAY DIFFRACTIONr_sphericity_bonded5.081104216
LS refinement shellResolution: 1.35→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.28 237
Rwork0.229 4703
obs-4703
Refinement
*PLUS
Rfactor Rfree: 0.173 / Rfactor Rwork: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.626

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