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- PDB-3ss1: Clostridium difficile toxin A (TcdA) glucolsyltransferase domain -

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Basic information

Entry
Database: PDB / ID: 3ss1
TitleClostridium difficile toxin A (TcdA) glucolsyltransferase domain
ComponentsToxin A
KeywordsTRANSFERASE / Glucosyltransferase
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / peptidase activity / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / peptidase activity / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding / plasma 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
: / Toxin A / Toxin A
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsPruitt, R.N. / Chumbler, N.M. / Farrow, M.A. / Seeback, S.A. / Friedman, D.B. / Spiller, B.W. / Lacy, D.B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural Determinants of Clostridium difficile Toxin A Glucosyltransferase Activity.
Authors: Pruitt, R.N. / Chumbler, N.M. / Rutherford, S.A. / Farrow, M.A. / Friedman, D.B. / Spiller, B. / Lacy, D.B.
History
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 13, 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 / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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 / _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)64,4552
Polymers64,4001
Non-polymers551
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.908, 141.908, 65.946
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: 64399.672 Da / Num. of mol.: 1 / Fragment: glucosyltransferase domain (UNP residues 1-542)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0663, CD630_06630, tcdA / Plasmid: pC-His1622 / Production host: Bacillus megaterium (bacteria) / Strain (production host): WH320
References: UniProt: Q189K5, UniProt: P16154*PLUS, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG3350, 0.2 M L-proline, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.0094 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2010
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0094 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 38544 / Num. obs: 38544 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3807 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BVM

2bvm


Resolution: 2.202→48.304 Å / SU ML: 0.64 / σ(F): 0 / Phase error: 22.38 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1943 5.21 %5% THROUGHOUT
Rwork0.1819 ---
all0.1843 38544 --
obs0.1843 37260 96.68 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.645 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3558 Å2-0 Å2-0 Å2
2--5.3558 Å2-0 Å2
3----2.7248 Å2
Refinement stepCycle: LAST / Resolution: 2.202→48.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 1 233 4637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074483
X-RAY DIFFRACTIONf_angle_d1.0046053
X-RAY DIFFRACTIONf_dihedral_angle_d15.3141698
X-RAY DIFFRACTIONf_chiral_restr0.072678
X-RAY DIFFRACTIONf_plane_restr0.004774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2017-2.25680.28631260.22572314X-RAY DIFFRACTION89
2.2568-2.31780.30471270.22182333X-RAY DIFFRACTION91
2.3178-2.3860.30641340.20982416X-RAY DIFFRACTION93
2.386-2.4630.28451320.20062449X-RAY DIFFRACTION95
2.463-2.5510.26261350.19872478X-RAY DIFFRACTION95
2.551-2.65310.26811390.20222549X-RAY DIFFRACTION97
2.6531-2.77390.2441370.20142512X-RAY DIFFRACTION98
2.7739-2.92010.24881400.19892550X-RAY DIFFRACTION98
2.9201-3.1030.2651450.20762577X-RAY DIFFRACTION99
3.103-3.34260.24251450.20042600X-RAY DIFFRACTION99
3.3426-3.67880.23781410.19282599X-RAY DIFFRACTION100
3.6788-4.21090.16641470.16082618X-RAY DIFFRACTION100
4.2109-5.30420.19331470.14272628X-RAY DIFFRACTION100
5.3042-48.3160.20491480.16642694X-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)
10.92360.4481-0.16431.9787-0.1611.40780.1798-0.24110.01240.285-0.1588-0.2207-0.41940.2689-0.02940.2659-0.18360.04680.3785-0.02870.28-8.165388.1073-15.6327
20.98480.2863-0.36170.7279-0.39411.3082-0.0832-0.1109-0.1418-0.0392-0.0892-0.09620.43040.41040.06910.18220.09360.02710.28520.05210.2469-21.344747.35797.8342
30.75980.01620.08291.4638-0.01260.2344-0.13770.3367-0.4125-0.7961-0.0978-0.28840.46420.48410.10220.76140.2430.24490.6732-0.09290.541-5.581638.8297-19.4472
40.9617-0.0541-0.26860.5068-0.39841.19450.01350.05760.07910.0119-0.0297-0.07560.01190.23670.00240.1064-0.0323-0.01090.2764-0.00880.1778-23.415762.6965-4.2382
55.2559-0.8929-2.35660.61531.00232.9514-0.42120.1069-0.066-0.02280.1576-0.09490.76320.37190.25670.5543-0.12610.06750.4168-0.12750.4039-34.709839.3075-6.6211
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:89)
2X-RAY DIFFRACTION2(chain A and resid 90:291)
3X-RAY DIFFRACTION3(chain A and resid 292:371)
4X-RAY DIFFRACTION4(chain A and resid 372:514)
5X-RAY DIFFRACTION5(chain A and resid 515:538)

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