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- PDB-4nbz: Crystal Structure of TcdA-A1 Bound to A26.8 VHH -

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Basic information

Entry
Database: PDB / ID: 4nbz
TitleCrystal Structure of TcdA-A1 Bound to A26.8 VHH
Components
  • A26.8 VHH
  • TcdA
KeywordsIMMUNE SYSTEM / Antibody-antigen complex
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / 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 ...Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium difficile (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMurase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E.N. / Klassen, J.S. / Ng, K.K.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile.
Authors: Murase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E.N. / Klassen, J.S. / Ng, K.K.
History
DepositionOct 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Sep 20, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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: TcdA
B: A26.8 VHH
C: TcdA
D: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)66,5984
Polymers66,5984
Non-polymers00
Water8,647480
1
A: TcdA
B: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)33,2992
Polymers33,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: TcdA
D: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)33,2992
Polymers33,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.002, 60.002, 133.935
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein TcdA


Mass: 16288.184 Da / Num. of mol.: 2 / Fragment: UNP residues 2573-2709
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 48489 / Gene: tcdA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I6YE93, UniProt: P16154*PLUS
#2: Antibody A26.8 VHH


Mass: 17010.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Gene: VHH / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1.5 M Lithium chloride, 12% (w/v) PEG 6000, 0.1 M Citric acid, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2010 / Details: mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 53882 / Num. obs: 53882 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.569 / Net I/σ(I): 11
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / Num. unique all: 3513 / Rsym value: 0.56 / % possible all: 95.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F6E

2f6e


Resolution: 1.75→33.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.905 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.139 / ESU R Free: 0.133 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24688 2763 5.1 %RANDOM
Rwork0.20597 ---
obs0.20809 51089 98.99 %-
all-51089 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.8 Å20 Å2
2--0.8 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4165 0 0 480 4645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.024272
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9235791
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03923.559222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7415638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4821530
X-RAY DIFFRACTIONr_chiral_restr0.0730.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213398
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 197 -
Rwork0.329 3410 -
obs--90.08 %

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