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- PDB-7lov: Crystal structure of Clostridium difficile Toxin B (TcdB) glucosy... -

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Basic information

Entry
Database: PDB / ID: 7lov
TitleCrystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and noeuromycin
ComponentsToxin B
KeywordsTRANSFERASE/Inhibitor / inhibitors / TcdB / toxin / Kinetic isotope effects / KIEs / drug design / TRANSFERASE / TRANSFERASE-Inhibitor complex
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
Similarity search - Domain/homology
: / Chem-NOY / URIDINE-5'-DIPHOSPHATE / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHarijan, R.K. / Paparella, A.S. / Aboulache, B.L. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Nat Commun / Year: 2021
Title: Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues.
Authors: Paparella, A.S. / Aboulache, B.L. / Harijan, R.K. / Potts, K.S. / Tyler, P.C. / Schramm, V.L.
History
DepositionFeb 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin B
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,33313
Polymers128,6282
Non-polymers1,70511
Water4,017223
1
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,2127
Polymers64,3141
Non-polymers8996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1206
Polymers64,3141
Non-polymers8065
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.589, 82.676, 113.227
Angle α, β, γ (deg.)90.000, 92.430, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0 / Auth seq-ID: 2 - 538 / Label seq-ID: 3 - 539

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Toxin B


Mass: 64313.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases

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Non-polymers , 5 types, 234 molecules

#2: Chemical ChemComp-NOY / (2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.7 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 85 mM Sodium Citrate pH 5.6, 170 mM Ammonium Acetate, 25.5 % (w/v) PEG 4000, 15 %(v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→28.97 Å / Num. obs: 48863 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.27 / Net I/σ(I): 6.2
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4458 / CC1/2: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UQM

5uqm


Resolution: 2.5→28.97 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 11.792 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.506 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 2334 4.8 %RANDOM
Rwork0.2081 ---
obs0.21 46524 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.17 Å2 / Biso mean: 39.964 Å2 / Biso min: 14.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.5 Å20 Å2-0.21 Å2
2---1.21 Å20 Å2
3----1.27 Å2
Refinement stepCycle: final / Resolution: 2.5→28.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8808 0 104 223 9135
Biso mean--37.92 31.44 -
Num. residues----1077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0139068
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178163
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.64912242
X-RAY DIFFRACTIONr_angle_other_deg1.1251.58119059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77951075
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27524.758517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.513151664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.531535
X-RAY DIFFRACTIONr_chiral_restr0.0440.21193
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021819
Refine LS restraints NCS

Ens-ID: 1 / Number: 18364 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.25 177 -
Rwork0.21 3402 -
obs--99.94 %

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