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- PDB-1pzi: Heat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Gal... -

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Basic information

Entry
Database: PDB / ID: 1pzi
TitleHeat-Labile Enterotoxin B-Pentamer Complexed With Nitrophenyl Galactoside 2a
ComponentsHeat-labile Enterotoxin B subunit
KeywordsTOXIN INHIBITOR / PENTAMER / MONOVALENT / TOXIN / INHIBITOR
Function / homology
Function and homology information


toxin activity / killing of cells of another organism / extracellular region
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-1DM / Heat-labile enterotoxin B chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 1.5Oct 16, 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: Heat-labile Enterotoxin B subunit
E: Heat-labile Enterotoxin B subunit
F: Heat-labile Enterotoxin B subunit
G: Heat-labile Enterotoxin B subunit
H: Heat-labile Enterotoxin B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,82110
Polymers59,0385
Non-polymers2,7835
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-53 kcal/mol
Surface area21230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.817, 78.683, 62.300
Angle α, β, γ (deg.)90.00, 116.20, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Heat-labile Enterotoxin B subunit / LT-B / LTP-B / porcine / Heat-labile Enterotoxin B chain


Mass: 11807.539 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ELTB / Plasmid: LAMBDA-PR / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P32890
#2: Chemical
ChemComp-1DM / N-(2-MORPHOLIN-4-YL-1-MORPHOLIN-4-YLMETHYL-ETHYL)-3-NITRO-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE


Mass: 556.563 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H36N4O11
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / 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: 1.96 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 32% PEG 5000, 100 mM Tris-HCl pH 7.8, 50 mM NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
132 %PEG50001drop
2100 mMTris-HCl1droppH7.8
350 mM1dropNaCl
45 mg/mlprotein1drop
510 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: SBC-2 / Detector: CCD / Date: Feb 23, 2002
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 34499 / Num. obs: 34499 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.45 % / Biso Wilson estimate: 20.322 Å2 / Rsym value: 0.061 / Net I/σ(I): 19.28
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 2.27 % / Mean I/σ(I) obs: 7.07 / Num. unique all: 3005 / Rsym value: 0.145 / % possible all: 84.1
Reflection
*PLUS
Num. measured all: 124930 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 84.1 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 7.1

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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: 1DJR

1djr


Resolution: 1.99→27.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.336 / SU ML: 0.121 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.192 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 1731 5 %RANDOM
Rwork0.15449 ---
all0.15778 34499 --
obs0.15778 32749 95.21 %-
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: 15.815 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.03 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.99→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 168 575 4863
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224358
X-RAY DIFFRACTIONr_bond_other_d0.0010.023809
X-RAY DIFFRACTIONr_angle_refined_deg1.1582.0095882
X-RAY DIFFRACTIONr_angle_other_deg0.6513.0018958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3385510
X-RAY DIFFRACTIONr_chiral_restr0.0670.2699
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024560
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02744
X-RAY DIFFRACTIONr_nbd_refined0.210.3931
X-RAY DIFFRACTIONr_nbd_other0.290.35042
X-RAY DIFFRACTIONr_nbtor_other0.0880.52395
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.5775
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.367
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.524
X-RAY DIFFRACTIONr_mcbond_it1.65642575
X-RAY DIFFRACTIONr_mcangle_it2.43364225
X-RAY DIFFRACTIONr_scbond_it3.01761783
X-RAY DIFFRACTIONr_scangle_it4.46181657
LS refinement shellResolution: 1.99→2.041 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.295 118
Rwork0.183 -
obs-2009
Refinement
*PLUS
Rfactor Rfree: 0.221 / Rfactor Rwork: 0.154
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.158

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