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

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Basic information

Entry
Database: PDB / ID: 5uqk
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 / metal ion binding / membrane
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: 1.851 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: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_validate_close_contact ...pdbx_audit_support / pdbx_validate_close_contact / struct_conn / struct_conn_type
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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
Water8,431468
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-8 kcal/mol
Surface area25220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.810, 142.810, 66.074
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-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
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 3.01 Å3/Da / Density % sol: 59.08 % / Description: Long, hexagonal bars.
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-D / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.85→31.4 Å / Num. obs: 65449 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.597 / Net I/σ(I): 28.4

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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: 1.851→31.4 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.32
RfactorNum. reflection% reflection
Rfree0.2071 1995 3.05 %
Rwork0.1817 --
obs0.1825 65417 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.851→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 37 468 4908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214699
X-RAY DIFFRACTIONf_angle_d1.5986398
X-RAY DIFFRACTIONf_dihedral_angle_d13.172919
X-RAY DIFFRACTIONf_chiral_restr0.102726
X-RAY DIFFRACTIONf_plane_restr0.014817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8513-1.89760.26821410.27914406X-RAY DIFFRACTION98
1.8976-1.94890.2871390.2834519X-RAY DIFFRACTION100
1.9489-2.00620.2541410.23214524X-RAY DIFFRACTION100
2.0062-2.0710.25011450.22384510X-RAY DIFFRACTION100
2.071-2.1450.24271380.20724503X-RAY DIFFRACTION100
2.145-2.23080.21691410.19164512X-RAY DIFFRACTION100
2.2308-2.33230.21741420.19294528X-RAY DIFFRACTION100
2.3323-2.45530.20891450.18294541X-RAY DIFFRACTION100
2.4553-2.6090.22921420.18254511X-RAY DIFFRACTION100
2.609-2.81040.2261430.1854545X-RAY DIFFRACTION100
2.8104-3.09290.24571440.18144550X-RAY DIFFRACTION100
3.0929-3.540.21121390.17284539X-RAY DIFFRACTION100
3.54-4.4580.16851490.15774580X-RAY DIFFRACTION100
4.458-31.41480.18041460.17134654X-RAY DIFFRACTION100
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)
10.1482-0.19260.21560.27930.2840.8908-0.0492-0.14820.0252-0.0326-0.1175-0.0093-0.2316-0.1894-0.11550.24010.0358-0.0190.2417-0.04260.251389.284775.88550.0332
20.4481-0.3187-0.01250.24080.25570.5632-0.05380.1507-0.04690.03610.0271-0.0303-0.02870.0135-0.00020.2214-0.03890.00280.31580.01210.243298.606859.2843-4.9183
30.63470.03590.08010.08710.10950.0677-0.12870.3074-0.10890.17220.019-0.0202-0.33460.0803-0.01140.6354-0.0986-0.02720.4460.10870.5246101.43983.1033-7.6849
40.17570.06860.51210.59440.34480.66840.0735-0.1055-0.0160.045-0.10980.19310.1989-0.1125-0.00740.2622-0.0450.02980.3856-0.030.328579.445841.1625-12.7958
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 108 through 418 )
2X-RAY DIFFRACTION2chain 'A' and (resid 419 through 506 )
3X-RAY DIFFRACTION3chain 'A' and (resid 507 through 538 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2 through 107 )

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