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- PDB-4r04: Clostridium difficile Toxin A (TcdA) -

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Basic information

Entry
Database: PDB / ID: 4r04
TitleClostridium difficile Toxin A (TcdA)
ComponentsToxin A
KeywordsTRANSFERASE / Glucosly Transferase
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
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. ...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
Similarity search - Domain/homology
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.26 Å
AuthorsLacy, D.B. / Spiller, B.W. / Rutherford, S.A.
CitationJournal: Nat Microbiol / Year: 2016
Title: Glucosyl Transferase Structure
Authors: Lacy, D.B. / Spiller, B.W. / Rutherford, S.A.
History
DepositionJul 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)209,9092
Polymers209,8441
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)303.490, 124.540, 75.950
Angle α, β, γ (deg.)90.00, 97.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Toxin A / Glucosyl Transferase


Mass: 209843.844 Da / Num. of mol.: 1 / Fragment: UNP residues 1-1832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Gene: Clostridium difficile, tcdA, toxA / References: UniProt: P16154
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 3.39 Å3/Da / Density % sol: 63.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 100 mM Bis-Tris, pH 5.8, 8% PEG 4000, 50 mM GuCl, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.2814 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2814 Å / Relative weight: 1
ReflectionResolution: 3.26→61.615 Å / Num. all: 43875 / Num. obs: 43830 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 6 % / Biso Wilson estimate: 106 Å2 / Rmerge(I) obs: 0.073
Reflection shellResolution: 3.26→3.34 Å / Redundancy: 6 % / Rmerge(I) obs: 0.829 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SHARPphasing
PHENIX(phenix.refine: dev_1565)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.26→61.615 Å / SU ML: 0.52 / σ(F): 1.35 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2495 1931 4.57 %
Rwork0.2206 --
obs0.2219 43830 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati sigma a obs: 0.52 Å
Refinement stepCycle: LAST / Resolution: 3.26→61.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14409 0 1 0 14410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314671
X-RAY DIFFRACTIONf_angle_d0.62819845
X-RAY DIFFRACTIONf_dihedral_angle_d9.8315466
X-RAY DIFFRACTIONf_chiral_restr0.0232264
X-RAY DIFFRACTIONf_plane_restr0.0022534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2601-3.29980.4191430.37032985X-RAY DIFFRACTION100
3.2998-3.34160.36241370.35112881X-RAY DIFFRACTION100
3.3416-3.38550.51811430.34482971X-RAY DIFFRACTION100
3.3855-3.43190.3581360.3312930X-RAY DIFFRACTION100
3.4319-3.48090.36411390.33762931X-RAY DIFFRACTION100
3.4809-3.53290.2871380.30252844X-RAY DIFFRACTION100
3.5329-3.58810.35341440.2962988X-RAY DIFFRACTION100
3.5881-3.64690.34271400.28582957X-RAY DIFFRACTION100
3.6469-3.70980.30121380.2832869X-RAY DIFFRACTION100
3.7098-3.77720.28531400.26732977X-RAY DIFFRACTION100
3.7772-3.84990.32341430.26352924X-RAY DIFFRACTION100
3.8499-3.92850.25641370.25082894X-RAY DIFFRACTION100
3.9285-4.01390.27991460.2492993X-RAY DIFFRACTION100
4.0139-4.10720.30681390.24272883X-RAY DIFFRACTION100
4.1072-4.20990.22771430.242966X-RAY DIFFRACTION100
4.2099-4.32370.20961370.21032909X-RAY DIFFRACTION100
4.3237-4.45090.21641440.20312930X-RAY DIFFRACTION100
4.4509-4.59450.1961400.19622893X-RAY DIFFRACTION100
4.5945-4.75870.23251410.19822970X-RAY DIFFRACTION100
4.7587-4.94910.24621410.21182910X-RAY DIFFRACTION100
4.9491-5.17430.27961400.20692945X-RAY DIFFRACTION100
5.1743-5.44690.21061410.20522942X-RAY DIFFRACTION100
5.4469-5.78790.23731430.22492903X-RAY DIFFRACTION100
5.7879-6.23440.2771390.2232911X-RAY DIFFRACTION100
6.2344-6.86110.33581430.23242979X-RAY DIFFRACTION100
6.8611-7.85220.25631400.21112923X-RAY DIFFRACTION100
7.8522-9.88630.15461410.16012915X-RAY DIFFRACTION100
9.8863-61.62640.17991360.15442897X-RAY DIFFRACTION99
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)
11.6626-0.6524-0.97882.07370.57831.86970.0729-0.47410.49950.61750.4266-0.81840.0490.6986-0.38751.01360.0902-0.21690.9878-0.43550.9957397.91691.37280.4363
22.7931-0.17741.63852.9706-2.15373.2409-0.1401-0.37820.4535-0.420.3754-0.30370.244-0.3592-0.23181.0568-0.07490.15810.963-0.18090.6239367.858988.309116.9214
32.63820.0594-2.51530.15-0.06722.8192-0.12540.06890.0661-0.12030.13650.16820.2166-0.3191-0.06050.7999-0.11710.0810.75930.0820.7533327.132992.5405125.0051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 877 )
2X-RAY DIFFRACTION2chain 'A' and (resid 878 through 974 )
3X-RAY DIFFRACTION3chain 'A' and (resid 975 through 1802 )

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