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- PDB-1pzj: Cholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5 -

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Basic information

Entry
Database: PDB / ID: 1pzj
TitleCholera Toxin B-Pentamer Complexed With Nitrophenyl Galactoside 5
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-15B / Chem-J15 / Cholera enterotoxin B-subunit
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 6, 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)60,75410
Polymers58,1165
Non-polymers2,6385
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14420 Å2
ΔGint-50 kcal/mol
Surface area22300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.754, 65.998, 77.362
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-1586-

HOH

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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-15B / N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-BETA-BENZAMIDE


Mass: 527.568 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H37N5O9
#3: Chemical ChemComp-J15 / N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-ALPHA-BENZAMIDE


Mass: 527.568 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H37N5O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 1.81 Å3/Da / Density % sol: 31.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 42% PEG 350, 50 mM NaCl, 100 mM Tris-HCl pH 7.5, 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
142 %PEG3501reservoir
250 mM1reservoirNaCl
3100 mMTris-HCl1reservoirpH7.5
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 18, 2002
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→99 Å / Num. all: 85036 / Num. obs: 85036 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.18 % / Biso Wilson estimate: 13.821 Å2 / Rsym value: 0.048 / Net I/σ(I): 19.74
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 2.46 % / Mean I/σ(I) obs: 8.601 / Num. unique all: 8013 / Rsym value: 0.115 / % possible all: 93.2
Reflection
*PLUS
Num. measured all: 274226 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 8.6

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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: 1.46→19.69 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.793 / SU ML: 0.032 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.059 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15925 4274 5 %RANDOM
Rwork0.11515 ---
all0.1174 85036 --
obs0.1174 80755 98.91 %-
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: 11.474 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.02 Å2
2---0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.46→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4095 0 185 650 4930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214380
X-RAY DIFFRACTIONr_bond_other_d0.0050.023870
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.9875930
X-RAY DIFFRACTIONr_angle_other_deg1.11139116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145510
X-RAY DIFFRACTIONr_chiral_restr0.0950.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024616
X-RAY DIFFRACTIONr_gen_planes_other0.0180.02768
X-RAY DIFFRACTIONr_nbd_refined0.2280.3846
X-RAY DIFFRACTIONr_nbd_other0.280.34630
X-RAY DIFFRACTIONr_nbtor_other0.0990.52331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5816
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.537
X-RAY DIFFRACTIONr_mcbond_it2.29932577
X-RAY DIFFRACTIONr_mcangle_it3.20744190
X-RAY DIFFRACTIONr_scbond_it4.97161793
X-RAY DIFFRACTIONr_scangle_it6.72681715
X-RAY DIFFRACTIONr_rigid_bond_restr2.46244370
X-RAY DIFFRACTIONr_sphericity_free21.28420650
X-RAY DIFFRACTIONr_sphericity_bonded6.274204280
LS refinement shellResolution: 1.46→1.496 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.173 317
Rwork0.101 5733
obs-5733
Refinement
*PLUS
Rfactor Rfree: 0.159 / Rfactor Rwork: 0.115
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d1.485

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