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

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Basic information

Entry
Database: PDB / ID: 3srz
TitleClostridium difficile toxin A (TcdA) glucolsyltransferase domain bound to UDP-glucose
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
: / URIDINE-5'-DIPHOSPHATE-GLUCOSE / Toxin A / Toxin A
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 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 1.3Feb 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_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)65,0213
Polymers64,4001
Non-polymers6212
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.779, 141.779, 63.351
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: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG6000, 0.1 M bicine, pH 8.0, VAPOR DIFFUSION, HANGING 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: 2.58→50 Å / Num. all: 23085 / Num. obs: 23039 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.5
Reflection shellResolution: 2.58→2.67 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2278 / % possible all: 99.4

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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 / Resolution: 2.58→40.928 Å / SU ML: 0.87 / Isotropic thermal model: ISOTROPIC / σ(F): 0 / σ(I): 0 / Phase error: 25.29 / Stereochemistry target values: ML / Details: PDB ENTRY 3SS1
RfactorNum. reflection% reflectionSelection details
Rfree0.2476 1914 8.62 %5% THROUGHOUT
Rwork0.1774 ---
all0.1835 23085 --
obs0.1835 22207 96.16 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.25 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.4957 Å2-0 Å2-0 Å2
2--4.4957 Å2-0 Å2
3----0.8231 Å2
Refine analyzeLuzzati d res low obs: 49 Å / Luzzati sigma a obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.58→40.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4403 0 37 109 4549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074521
X-RAY DIFFRACTIONf_angle_d1.0876111
X-RAY DIFFRACTIONf_dihedral_angle_d16.7131718
X-RAY DIFFRACTIONf_chiral_restr0.068687
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5804-2.64490.38641170.28311279X-RAY DIFFRACTION85
2.6449-2.71640.34391250.24711359X-RAY DIFFRACTION90
2.7164-2.79630.30411310.21891388X-RAY DIFFRACTION94
2.7963-2.88660.28631410.22251393X-RAY DIFFRACTION93
2.8866-2.98970.32541290.21111426X-RAY DIFFRACTION96
2.9897-3.10940.33421400.22321425X-RAY DIFFRACTION95
3.1094-3.25080.31041390.2011470X-RAY DIFFRACTION98
3.2508-3.42210.26021360.1891457X-RAY DIFFRACTION98
3.4221-3.63640.24551420.1841510X-RAY DIFFRACTION99
3.6364-3.9170.24041400.17781484X-RAY DIFFRACTION99
3.917-4.31080.22821490.14791511X-RAY DIFFRACTION100
4.3108-4.93370.16871420.12461503X-RAY DIFFRACTION100
4.9337-6.21240.23831400.17151537X-RAY DIFFRACTION100
6.2124-40.93320.19741430.15121551X-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)
14.05651.29042.11041.72710.0753.36730.07830.0326-0.0114-0.04590.17740.26250.3193-0.3544-0.19930.10090.0673-0.07520.27620.08480.0954-72.6672-51.7446-25.0266
21.58870.16320.45711.3947-0.32871.7102-0.05770.10390.2044-0.0685-0.0915-0.2096-0.33130.35320.03760.1-0.0515-0.10530.03120.10850.1553-29.9081-41.8312-5.2902
31.68841.0856-0.40081.41360.59721.1872-0.13260.56520.4816-0.45740.2480.018-0.64030.1243-0.13510.5103-0.0782-0.04860.3760.15210.2858-32.1984-30.0861-29.9217
41.6907-0.73411.74451.9142-0.96861.96890.14570.2528-0.0386-0.1581-0.1171-0.04690.03190.1612-0.03290.14420.08820.05410.2022-0.01260.1115-43.0382-55.2475-13.458
51.204-0.91991.05981.2959-1.03791.0207-0.2344-0.3405-0.85220.1492-0.1192-0.20470.21990.72940.42120.39710.12320.19440.82080.30460.6117-20.1571-47.1288-18.9252
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:87)
2X-RAY DIFFRACTION2(chain A and resid 88:298)
3X-RAY DIFFRACTION3(chain A and resid 299:390)
4X-RAY DIFFRACTION4(chain A and resid 391:506)
5X-RAY DIFFRACTION5(chain A and resid 507:538)

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