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- PDB-5uqn: Clostridium difficile Toxin B (TcdB) glucosyltransferase domain i... -

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Basic information

Entry
Database: PDB / ID: 5uqn
TitleClostridium difficile Toxin B (TcdB) glucosyltransferase domain in complex with U2F
ComponentsToxin B
KeywordsTRANSFERASE / Glucosyltransferase / Toxin / HYDROLASE
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 / 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 ...Arc Repressor Mutant, subunit A - #1780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1190 / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Arc Repressor Mutant, subunit A / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-U2F / Toxin B
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsAlvin, J.W. / Lacy, D.B.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Veterans AffairsBX02943 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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1725
Polymers65,3571
Non-polymers8154
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-34 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 62.390, 328.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Toxin B


Mass: 65356.988 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23FN2O16P2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.44 Å3/Da / Density % sol: 49.63 % / Description: Short bars.
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M MES, 0.2 M ammonium sulfate, PEG 8k 16-34% / PH range: 6-6.5

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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: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.06→54.67 Å / Num. obs: 41228 / % possible obs: 99.1 % / Redundancy: 11.2 % / CC1/2: 0.946 / Rmerge(I) obs: 0.069 / Net I/σ(I): 23.2

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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: 2BVL

2bvl


Resolution: 2.06→54.19 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2343 2000 4.87 %
Rwork0.203 --
obs0.2044 41070 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.06→54.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4429 0 47 238 4714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084644
X-RAY DIFFRACTIONf_angle_d1.0156294
X-RAY DIFFRACTIONf_dihedral_angle_d15.1462833
X-RAY DIFFRACTIONf_chiral_restr0.051688
X-RAY DIFFRACTIONf_plane_restr0.004815
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.11150.29971300.26352544X-RAY DIFFRACTION93
2.1115-2.16860.30031350.26132634X-RAY DIFFRACTION96
2.1686-2.23240.28631400.24572738X-RAY DIFFRACTION99
2.2324-2.30450.25911410.22482748X-RAY DIFFRACTION99
2.3045-2.38690.30991410.22642764X-RAY DIFFRACTION100
2.3869-2.48240.25241420.22582768X-RAY DIFFRACTION100
2.4824-2.59540.22181440.22152815X-RAY DIFFRACTION100
2.5954-2.73220.26031410.22282764X-RAY DIFFRACTION100
2.7322-2.90340.26631430.22292797X-RAY DIFFRACTION100
2.9034-3.12760.23161450.20942837X-RAY DIFFRACTION100
3.1276-3.44230.24051440.21272820X-RAY DIFFRACTION100
3.4423-3.94020.21371470.18292863X-RAY DIFFRACTION100
3.9402-4.96380.17151480.15812903X-RAY DIFFRACTION99
4.9638-54.20840.23941590.1923075X-RAY DIFFRACTION98
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)
11.0653-0.1752-0.52230.8661-0.2850.89890.12320.49610.1672-0.1022-0.2326-0.2224-0.29890.736-0.01190.2548-0.15740.01660.84560.14050.325521.961713.4037-33.9864
20.5333-0.1660.1110.76210.41981.54880.00860.2993-0.0934-0.0413-0.10060.0428-0.06160.06660.08220.1597-0.0256-0.01360.3395-0.05160.27123.15660.2437-25.1745
31.0761-0.7804-0.62672.0569-0.81321.8477-0.1408-0.06190.68760.0665-0.04720.5404-0.5772-0.567600.4010.1476-0.1080.3835-0.15410.6223-15.004424.5176-2.9284
40.92870.00510.22411.12050.33681.8834-0.07230.2833-0.1678-0.02330.0018-0.02240.18850.42780.03670.1309-0.01770.01190.36680.00370.271912.383-7.0832-21.1422
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 358 )
2X-RAY DIFFRACTION2chain 'A' and (resid 359 through 542 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 264 )

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