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- PDB-5uql: Clostridium difficile toxin A (TcdA) glucosyltransferase domain i... -

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Basic information

Entry
Database: PDB / ID: 5uql
TitleClostridium difficile toxin A (TcdA) glucosyltransferase domain in complex with U2F
ComponentsToxin A
KeywordsTRANSFERASE / glucosyltransferase / toxin
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / 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 ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / 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
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 / 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 ...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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Chem-U2F / Toxin A
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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 A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3363
Polymers64,7131
Non-polymers6232
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-10 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.116, 142.116, 63.003
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Toxin A


Mass: 64712.988 Da / Num. of mol.: 1 / Fragment: residues 1-544
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: toxA, tcdA / Plasmid: pHIS1622 / Production host: Bacillus megaterium (bacteria)
References: UniProt: P16154, 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: isolated from a natural source / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 0.2 M L-proline PEG 3350, 10-25% / PH range: 7-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.97→46.518 Å / Num. obs: 51462 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.576 / Net I/σ(I): 21.35

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SRZ

3srz


Resolution: 1.97→46.518 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2039 1995 3.88 %
Rwork0.1841 --
obs0.1849 51428 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→46.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4433 0 37 428 4898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044675
X-RAY DIFFRACTIONf_angle_d0.6656344
X-RAY DIFFRACTIONf_dihedral_angle_d16.7421801
X-RAY DIFFRACTIONf_chiral_restr0.041714
X-RAY DIFFRACTIONf_plane_restr0.003807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9697-2.0190.3231370.29133485X-RAY DIFFRACTION99
2.019-2.07360.29371390.26343491X-RAY DIFFRACTION100
2.0736-2.13460.27131410.24623517X-RAY DIFFRACTION100
2.1346-2.20350.23391470.23943501X-RAY DIFFRACTION100
2.2035-2.28220.25791420.21443515X-RAY DIFFRACTION100
2.2822-2.37360.25011400.2153508X-RAY DIFFRACTION100
2.3736-2.48160.1961420.19433513X-RAY DIFFRACTION100
2.4816-2.61250.22141470.19633534X-RAY DIFFRACTION100
2.6125-2.77610.22461430.18873540X-RAY DIFFRACTION100
2.7761-2.99040.20931420.18443526X-RAY DIFFRACTION100
2.9904-3.29130.23361430.18193555X-RAY DIFFRACTION100
3.2913-3.76740.18151430.16323537X-RAY DIFFRACTION100
3.7674-4.74570.16351430.14353578X-RAY DIFFRACTION100
4.7457-46.53130.1651460.17173633X-RAY DIFFRACTION100

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