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- PDB-4np4: Clostridium difficile toxin B CROP domain in complex with FAB dom... -

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Basic information

Entry
Database: PDB / ID: 4np4
TitleClostridium difficile toxin B CROP domain in complex with FAB domains of neutralizing antibody bezlotoxumab
Components
  • Toxin B
  • bezlotoxumab heavy chain
  • bezlotoxumab light chain
KeywordsIMMUNE SYSTEM / bezlotoxumab / human antibody / FAB / CROP domain / cytotoxin / short repeat / long repeat / TcdB / receptor binding
Function / homology
Function and homology information


glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily ...Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsOrth, P. / Xiao, L. / Hernandez, L.D. / Reichert, P. / Sheth, P. / Beaumont, M. / Murgolo, N. / Ermakov, G. / DiNunzio, E. / Racine, F. ...Orth, P. / Xiao, L. / Hernandez, L.D. / Reichert, P. / Sheth, P. / Beaumont, M. / Murgolo, N. / Ermakov, G. / DiNunzio, E. / Racine, F. / Karczewski, J. / Secore, S. / Ingram, R.N. / Mayhood, T. / Strickland, C. / Therien, A.G.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Mechanism of Action and Epitopes of Clostridium difficile Toxin B-neutralizing Antibody Bezlotoxumab Revealed by X-ray Crystallography.
Authors: Orth, P. / Xiao, L. / Hernandez, L.D. / Reichert, P. / Sheth, P.R. / Beaumont, M. / Yang, X. / Murgolo, N. / Ermakov, G. / DiNunzio, E. / Racine, F. / Karczewski, J. / Secore, S. / Ingram, R. ...Authors: Orth, P. / Xiao, L. / Hernandez, L.D. / Reichert, P. / Sheth, P.R. / Beaumont, M. / Yang, X. / Murgolo, N. / Ermakov, G. / DiNunzio, E. / Racine, F. / Karczewski, J. / Secore, S. / Ingram, R.N. / Mayhood, T. / Strickland, C. / Therien, A.G.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 16, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
H: bezlotoxumab heavy chain
I: bezlotoxumab heavy chain
L: bezlotoxumab light chain
M: bezlotoxumab light chain


Theoretical massNumber of molelcules
Total (without water)126,2195
Polymers126,2195
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.413, 134.659, 102.579
Angle α, β, γ (deg.)90.00, 112.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Toxin B


Mass: 31657.363 Da / Num. of mol.: 1 / Fragment: CROP domain(UNP residues 1834-2099) / Source method: isolated from a natural source / Source: (natural) Clostridium difficile (bacteria) / References: UniProt: P18177
#2: Antibody bezlotoxumab heavy chain


Mass: 23829.766 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#3: Antibody bezlotoxumab light chain


Mass: 23450.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 4.01 Å3/Da / Density % sol: 69.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5
Details: 4% PEG 4000, pH 7.5, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2013
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.89→47.365 Å / Num. obs: 44417 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 97.68 Å2
Reflection shellResolution: 2.89→2.9 Å / % possible all: 1

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Processing

Software
NameVersionClassification
JDirectordata collection
AMoREphasing
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEG

3qeg


Resolution: 2.89→42.31 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9189 / SU R Cruickshank DPI: 0.543 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 931 2.1 %RANDOM
Rwork0.1979 ---
obs0.1987 44385 99.37 %-
all-44666 --
Displacement parametersBiso mean: 74.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.6893 Å20 Å2-15.8326 Å2
2--2.0021 Å20 Å2
3----0.3128 Å2
Refine analyzeLuzzati coordinate error obs: 0.414 Å
Refinement stepCycle: LAST / Resolution: 2.89→42.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 0 13 8686
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018903HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.3312122HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2883SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes206HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1312HARMONIC5
X-RAY DIFFRACTIONt_it8903HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion22.29
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9424SEMIHARMONIC4
LS refinement shellResolution: 2.89→2.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2908 76 2.31 %
Rwork0.2648 3216 -
all0.2654 3292 -
obs--99.37 %

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