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- PDB-7u1z: Crystal structure of the DRBD and CROPs of TcdA -

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Basic information

Entry
Database: PDB / ID: 7u1z
TitleCrystal structure of the DRBD and CROPs of TcdA
ComponentsToxin A
KeywordsTOXIN / TcdA / Toxin A
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, 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 ...Cholin Binding / left handed beta-beta-3-solenoid / 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 / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsBaohua, C. / Peng, C. / Kay, P. / Rongsheng, J.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125704 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI156092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI163178 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124165 United States
CitationJournal: Life Sci Alliance / Year: 2022
Title: Structure and conformational dynamics of Clostridioides difficile toxin A.
Authors: Chen, B. / Basak, S. / Chen, P. / Zhang, C. / Perry, K. / Tian, S. / Yu, C. / Dong, M. / Huang, L. / Bowen, M.E. / Jin, R.
History
DepositionFeb 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Mar 30, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Toxin A
A: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)375,33338
Polymers371,8752
Non-polymers3,45836
Water00
1
B: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,85921
Polymers185,9371
Non-polymers1,92120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Toxin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,47417
Polymers185,9371
Non-polymers1,53716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)379.507, 187.641, 95.324
Angle α, β, γ (deg.)90.000, 101.297, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Toxin A


Mass: 185937.297 Da / Num. of mol.: 2 / Fragment: UNP residues 843-2481
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdA, toxA / Production host: Escherichia coli (E. coli)
References: UniProt: P16154, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.54 Å3/Da / Density % sol: 72.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 6.3, 0.6 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.18→186.1 Å / Num. obs: 108739 / % possible obs: 99.07 % / Redundancy: 3.5 % / Biso Wilson estimate: 59.58 Å2 / CC1/2: 0.944 / Rmerge(I) obs: 0.283 / Net I/σ(I): 4.43
Reflection shellResolution: 3.18→3.29 Å / Rmerge(I) obs: 1.14 / Num. unique obs: 10768 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHENIXphasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r04, 4NP4, 2G7C

4r04

4np4

2g7c


Resolution: 3.18→186.08 Å / SU ML: 0.4393 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6077
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 5513 5.07 %
Rwork0.2066 103226 -
obs0.2091 108739 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.43 Å2
Refinement stepCycle: LAST / Resolution: 3.18→186.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25441 0 180 0 25621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.010626162
X-RAY DIFFRACTIONf_angle_d1.212235584
X-RAY DIFFRACTIONf_chiral_restr0.07313930
X-RAY DIFFRACTIONf_plane_restr0.00814564
X-RAY DIFFRACTIONf_dihedral_angle_d6.73873480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.210.38811710.33013083X-RAY DIFFRACTION90.46
3.21-3.250.35411920.31733418X-RAY DIFFRACTION98.99
3.25-3.290.32951630.28733515X-RAY DIFFRACTION99.14
3.29-3.330.34021840.27693404X-RAY DIFFRACTION99.58
3.33-3.380.29721740.27223457X-RAY DIFFRACTION99.1
3.38-3.420.32471730.27733456X-RAY DIFFRACTION98.21
3.42-3.470.30851930.25683298X-RAY DIFFRACTION96.65
3.47-3.520.31711640.25853479X-RAY DIFFRACTION98.7
3.52-3.580.32871690.25083430X-RAY DIFFRACTION99.47
3.58-3.640.30061940.243465X-RAY DIFFRACTION99.84
3.64-3.70.30311620.23453501X-RAY DIFFRACTION99.57
3.7-3.770.26892030.21743454X-RAY DIFFRACTION99.78
3.77-3.840.25761770.21233459X-RAY DIFFRACTION99.84
3.84-3.920.26661760.21023469X-RAY DIFFRACTION99.78
3.92-40.25831740.19993469X-RAY DIFFRACTION99.73
4-4.10.24081800.19143462X-RAY DIFFRACTION99.43
4.1-4.20.22661970.18193428X-RAY DIFFRACTION99.12
4.2-4.310.21042130.17023459X-RAY DIFFRACTION99.27
4.31-4.440.22132130.16353374X-RAY DIFFRACTION98.95
4.44-4.580.22571970.15793385X-RAY DIFFRACTION96.65
4.58-4.750.19371890.15773454X-RAY DIFFRACTION99.64
4.75-4.940.21332040.16263459X-RAY DIFFRACTION99.84
4.94-5.160.22482120.173451X-RAY DIFFRACTION99.75
5.16-5.430.22181720.18423468X-RAY DIFFRACTION99.37
5.43-5.770.21861670.1913476X-RAY DIFFRACTION99.56
5.77-6.220.30281710.22113503X-RAY DIFFRACTION99.16
6.22-6.850.2821750.22973436X-RAY DIFFRACTION97.62
6.85-7.840.27491930.2263481X-RAY DIFFRACTION99.86
7.84-9.870.211710.17353526X-RAY DIFFRACTION99.84
9.87-186.080.20931900.17983507X-RAY DIFFRACTION97.96

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