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- PDB-6oq5: Structure of the full-length Clostridium difficile toxin B in com... -

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Basic information

Entry
Database: PDB / ID: 6oq5
TitleStructure of the full-length Clostridium difficile toxin B in complex with 3 VHHs
Components
  • 5D
  • 7F
  • E3
  • Toxin B
KeywordsTOXIN / Toxin VHH
Function / homology
Function and homology information


host cell cytosol / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / membrane
Similarity search - Function
MARTX cysteine protease (CPD) domain / Arc Repressor Mutant, subunit A - #1780 / Cholin Binding / left handed beta-beta-3-solenoid / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization 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 ...MARTX cysteine protease (CPD) domain / Arc Repressor Mutant, subunit A - #1780 / Cholin Binding / left handed beta-beta-3-solenoid / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization 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 / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Ribbon / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glycosylating toxin TcdB
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Camelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.87 Å
AuthorsChen, P. / Lam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structure of the full-length Clostridium difficile toxin B.
Authors: Chen, P. / Lam, K.H. / Liu, Z. / Mindlin, F.A. / Chen, B. / Gutierrez, C.B. / Huang, L. / Zhang, Y. / Hamza, T. / Feng, H. / Matsui, T. / Bowen, M.E. / Perry, K. / Jin, R.
History
DepositionApr 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
D: 5D
E: E3
F: 7F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,3146
Polymers317,2244
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.619, 168.565, 179.921
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Toxin B


Mass: 270380.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB / Production host: Bacillus megaterium (bacteria) / References: UniProt: M4NKV9

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Antibody , 3 types, 3 molecules DEF

#2: Antibody 5D


Mass: 16864.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#3: Antibody E3


Mass: 14678.397 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#4: Antibody 7F


Mass: 15300.087 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY

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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: 3.58 Å3/Da / Density % sol: 65.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, 0.1M magnesium acetate, and 5% PEG 8K (final pH 5.2)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.87→48.91 Å / Num. obs: 42971 / % possible obs: 99.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 7.7
Reflection shellResolution: 3.87→3.97 Å / Rmerge(I) obs: 1.548 / Num. unique obs: 2123

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVL, 4R04, 3PEE, 6C0B, 3V0A, 4NP4, and 4NC2

2bvl

4r04

3pee

6c0b

3v0a

4np4

4nc2


Resolution: 3.87→48.91 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.902 / SU B: 81.488 / SU ML: 1.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.903
RfactorNum. reflection% reflectionSelection details
Rfree0.31516 2203 5.1 %RANDOM
Rwork0.26275 ---
obs0.26541 40731 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 169.399 Å2
Baniso -1Baniso -2Baniso -3
1--2.6 Å20 Å20 Å2
2--2.48 Å20 Å2
3---0.13 Å2
Refinement stepCycle: 1 / Resolution: 3.87→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21501 0 2 0 21503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01221924
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.62829682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.89152689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59124.7611174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.806153824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6991569
X-RAY DIFFRACTIONr_chiral_restr0.0930.22904
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216774
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.11416.86410774
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.57225.28913457
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7151711150
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined21.70188999
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.866→3.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 183 -
Rwork0.403 2894 -
obs--96.88 %

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