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- PDB-2qj6: Crystal structure analysis of a 14 repeat C-terminal fragment of ... -

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Basic information

Entry
Database: PDB / ID: 2qj6
TitleCrystal structure analysis of a 14 repeat C-terminal fragment of toxin TcdA in Clostridium difficile
ComponentsToxin A
KeywordsTOXIN / Clostridial Repetitive Oligo Peptides
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
Cholin Binding / left handed beta-beta-3-solenoid / 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 ...Cholin Binding / left handed beta-beta-3-solenoid / 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 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlbesa-Jove, D. / Bertrand, T. / Carpenter, L. / Lim, J. / Brown, K.A. / Fairweather, N.
CitationJournal: To be Published
Title: Solution and crystal structures of the cell binding domain of toxins TcdA and TcdB from Clostridium difficile
Authors: Albesa-Jove, D. / Bertrand, T. / Carpenter, L. / Lim, J. / Martinez, E. / Zhang, J. / Dmitri, I. / Brown, K.A. / Fairweather, N.
History
DepositionJul 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details
Remark 700SHEET DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin A
B: Toxin A


Theoretical massNumber of molelcules
Total (without water)74,4802
Polymers74,4802
Non-polymers00
Water3,297183
1
A: Toxin A


Theoretical massNumber of molelcules
Total (without water)37,2401
Polymers37,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Toxin A


Theoretical massNumber of molelcules
Total (without water)37,2401
Polymers37,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.050, 199.680, 58.720
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 16:74 or resseq 76:97 or resseq 99:332 )
21chain A and (resseq 16:74 or resseq 76:97 or resseq 99:332 )
31chain A and (resseq 16:74 or resseq 76:97 or resseq 99:332 )
12chain B and (resseq 16:74 or resseq 76:97 or resseq 99:332 )
22chain B and (resseq 16:74 or resseq 76:97 or resseq 99:332 )
32chain B and (resseq 16:74 or resseq 76:97 or resseq 99:332 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYLYSLYSAA16 - 7416 - 74
21TYRTYRTYRTYRAA76 - 9776 - 97
31ASNASNPROPROAA99 - 33299 - 332
12GLYGLYLYSLYSBB16 - 7416 - 74
22TYRTYRTYRTYRBB76 - 9776 - 97
32ASNASNPROPROBB99 - 33299 - 332

NCS ensembles :
IDDetails
1A
2B
DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit (chains A and B).

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Components

#1: Protein Toxin A


Mass: 37240.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: toxA, tcdA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16154
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 3.16 Å3/Da / Density % sol: 61.08 %
Crystal growTemperature: 293 K
Details: 0.2 M magnesium formate, 30 % (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2004
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinType: pseudo-merohedral / Operator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.5→56.3 Å / Num. obs: 29193 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.413 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.84
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.12 / % possible all: 80.4

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å44.24 Å
Translation3.5 Å44.24 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PHASER1.3.1phasing
CNS1.2refinement
PDB_EXTRACT2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G7C
Resolution: 2.5→56.335 Å / Isotropic thermal model: ISOTROPIC / Phase error: 25.1 / Stereochemistry target values: TWIN_LSQ_F
Details: The structure factor file contains twinned data with twinning operator= h,-k,-l and twinning fraction= 0.500.
RfactorNum. reflection% reflection
Rfree0.2734 1308 4.48 %
Rwork0.2256 --
obs0.2277 29193 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.909 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 29.138 Å2
Baniso -1Baniso -2Baniso -3
1--6.528 Å20 Å22.182 Å2
2--29.107 Å20 Å2
3----22.579 Å2
Refinement stepCycle: LAST / Resolution: 2.5→56.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5044 0 0 183 5227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065192
X-RAY DIFFRACTIONf_angle_d0.9637034
X-RAY DIFFRACTIONf_dihedral_angle_d18.2241740
X-RAY DIFFRACTIONf_chiral_restr0.074698
X-RAY DIFFRACTIONf_plane_restr0.003928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 98 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.5580.352830.2815821665
2.558-2.6220.276650.25516751740
2.622-2.6930.2961050.24416581763
2.693-2.7720.236660.22517101776
2.772-2.8620.317840.23117921876
2.862-2.9640.237790.22217811860
2.964-3.0830.295730.21418931966
3.083-3.2230.241990.21118631962
3.223-3.3930.236800.219602040
3.393-3.6050.269970.20519722069
3.605-3.8840.276780.20519882066
3.884-4.2740.2661290.19719672096
4.274-4.8930.2371170.20719872104
4.893-6.1630.31620.25520262088
6.163-56.3490.315910.28520312122
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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