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- PDB-5uqt: Clostridium difficile Toxin B (TcdB) glucosyltransferase domain c... -

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Basic information

Entry
Database: PDB / ID: 5uqt
TitleClostridium difficile Toxin B (TcdB) glucosyltransferase domain co-crystallized with apigenin
ComponentsToxin B
KeywordsTRANSFERASE / glucosyltransferase / toxin
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
Arc Repressor Mutant, subunit A - #1780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain ...Arc Repressor Mutant, subunit A - #1780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AGI / : / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAlvin, J.W. / Lacy, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Veterans AffairsBx002943 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI095755 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008320 United States
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Clostridium difficile toxin glucosyltransferase domains in complex with a non-hydrolyzable UDP-glucose analogue.
Authors: Alvin, J.W. / Lacy, D.B.
History
DepositionFeb 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)131,0945
Polymers130,7142
Non-polymers3803
Water00
1
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4122
Polymers65,3571
Non-polymers551
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6823
Polymers65,3571
Non-polymers3252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.090, 154.810, 271.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Toxin B


Mass: 65356.988 Da / Num. of mol.: 2 / Fragment: residues 1-543
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: toxB, tcdB / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-AGI / 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one / Apigenin


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5

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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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES pH 7.5-8.5, 0.2 M Mg(CH3CHOO)2, PEG 3350 5-25%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.75→44.437 Å / Num. obs: 45388 / % possible obs: 99.75 % / Redundancy: 6.6 % / CC1/2: 0.549 / Net I/σ(I): 21.33

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVM

2bvm


Resolution: 2.75→44.437 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 1978 4.37 %
Rwork0.1964 --
obs0.1981 45276 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.75→44.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8820 0 22 0 8842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079004
X-RAY DIFFRACTIONf_angle_d0.90612154
X-RAY DIFFRACTIONf_dihedral_angle_d21.5953393
X-RAY DIFFRACTIONf_chiral_restr0.0531322
X-RAY DIFFRACTIONf_plane_restr0.0061583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.81880.45291370.38683078X-RAY DIFFRACTION100
2.8188-2.8950.36841500.32833006X-RAY DIFFRACTION100
2.895-2.98020.31071280.28173076X-RAY DIFFRACTION100
2.9802-3.07630.29991520.26293055X-RAY DIFFRACTION100
3.0763-3.18630.281300.25223066X-RAY DIFFRACTION100
3.1863-3.31380.28141450.25623070X-RAY DIFFRACTION100
3.3138-3.46460.29011360.22793092X-RAY DIFFRACTION100
3.4646-3.64710.25051450.20633077X-RAY DIFFRACTION100
3.6471-3.87550.24071380.19533088X-RAY DIFFRACTION100
3.8755-4.17450.20341430.17753108X-RAY DIFFRACTION100
4.1745-4.59420.1921480.15783105X-RAY DIFFRACTION100
4.5942-5.25810.20811310.15983110X-RAY DIFFRACTION100
5.2581-6.62120.23141520.20423160X-RAY DIFFRACTION100
6.6212-44.44330.21141430.16623207X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8961-1.6472-0.50153.2168-0.42681.3272-0.3864-0.2273-0.81990.1720.24480.24410.83780.16890.09021.21560.12780.10740.52410.08581.1259109.5164-3.805819.9467
21.6719-0.29310.25881.66140.90022.3114-0.0991-0.13350.17540.1190.0428-0.0096-0.1399-0.30260.08580.44660.0246-0.02630.5078-0.01920.680797.723542.550214.2491
36.90060.46210.83992.6121-1.00773.4621-0.13160.8220.1446-0.30810.1288-0.0594-0.31140.40450.00760.5268-0.0933-0.03410.53540.00730.6736110.281536.287-14.7153
41.6685-0.0729-0.04721.14160.45562.4876-0.0549-0.1879-0.220.15410.1117-0.13650.24810.1456-0.04580.5092-0.0189-0.03730.4417-0.00330.7242107.803127.58912.8327
51.67160.82742.07960.50791.23843.0566-0.1195-0.42220.0251-0.0317-0.07430.4682-0.5308-0.22850.08770.6887-0.10260.01160.8766-0.06940.8211115.634450.71348.3871
61.25040.77210.24740.9494-0.44060.8983-0.34790.0275-0.35920.12920.6287-0.34410.99111.6554-0.31731.39930.766-0.31961.6526-0.35370.9159148.846913.414132.3518
72.1589-1.26970.67853.49330.50094.54730.0775-0.24550.2390.57080.2711-0.2028-0.03921.0705-0.24860.812-0.0351-0.08371.0905-0.29260.7255136.922542.386251.5203
83.24470.3911-0.06630.5070.98052.37940.0841-1.0876-0.78660.4721-0.2479-0.21761.83320.30130.01242.55770.6704-0.49361.4852-0.07620.8476136.959811.135769.8265
94.52-1.24920.59492.701-0.35722.48440.18760.28940.45570.06660.2017-0.76690.73831.3958-0.22590.79450.3694-0.23471.1475-0.30010.5582137.44830.53637.0977
101.8997-1.4060.23735.0505-0.07691.26680.29160.6408-0.52540.1346-0.21250.69360.70530.1176-0.09070.86380.3276-0.16181.1597-0.23290.7442132.548726.029535.8027
111.77920.3440.82150.7148-0.77421.67610.5934-0.09650.06990.0264-0.31050.28830.7111-0.0724-0.29471.30970.1584-0.07781.1488-0.02520.7471127.883925.791454.879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 88 )
2X-RAY DIFFRACTION2chain 'A' and (resid 89 through 298 )
3X-RAY DIFFRACTION3chain 'A' and (resid 299 through 339 )
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 512 )
5X-RAY DIFFRACTION5chain 'A' and (resid 513 through 539 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2 through 137 )
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 298 )
8X-RAY DIFFRACTION8chain 'B' and (resid 299 through 366 )
9X-RAY DIFFRACTION9chain 'B' and (resid 367 through 438 )
10X-RAY DIFFRACTION10chain 'B' and (resid 439 through 494 )
11X-RAY DIFFRACTION11chain 'B' and (resid 495 through 539 )

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