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- PDB-4nc1: Crystal Structure of TcdA-A2 Bound to A20.1 VHH and A26.8 VHH -

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Basic information

Entry
Database: PDB / ID: 4nc1
TitleCrystal Structure of TcdA-A2 Bound to A20.1 VHH and A26.8 VHH
Components
  • A20.1 VHH
  • A26.8 VHH
  • Cell wall-binding repeat protein
KeywordsIMMUNE SYSTEM / Antibody-antigen complex
Function / homologyCholin Binding / left handed beta-beta-3-solenoid / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesClostridium difficile (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell wall-binding repeat protein
C: A20.1 VHH
E: A26.8 VHH
B: Cell wall-binding repeat protein
D: A20.1 VHH
F: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)121,9396
Polymers121,9396
Non-polymers00
Water97354
1
A: Cell wall-binding repeat protein
C: A20.1 VHH
E: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)60,9693
Polymers60,9693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell wall-binding repeat protein
D: A20.1 VHH
F: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)60,9693
Polymers60,9693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.020, 122.290, 247.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cell wall-binding repeat protein


Mass: 29547.760 Da / Num. of mol.: 2 / Fragment: UNP residues 1-248
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 48489 / Gene: HMPREF0219_0762, TcdA / Production host: Escherichia coli (E. coli) / References: UniProt: D5RWT1
#2: Antibody A20.1 VHH


Mass: 16828.449 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: Antibody A26.8 VHH


Mass: 14593.076 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 20% (w/v) PEG 4000, 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: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 5, 2012 / 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: 2.61→40 Å / Num. all: 47857 / Num. obs: 47857 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 24.5
Reflection shellResolution: 2.61→2.68 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2284 / Rsym value: 0.719 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G7C

2g7c


Resolution: 2.61→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.456 / SU ML: 0.205 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.379 / ESU R Free: 0.274 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2524 2487 5.2 %RANDOM
Rwork0.20233 ---
obs0.2049 45426 99.94 %-
all-45426 --
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: 60.044 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å20 Å20 Å2
2--0.69 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.61→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7504 0 0 54 7558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.027702
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.91910445
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62423.616401
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.436151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3951551
X-RAY DIFFRACTIONr_chiral_restr0.0790.21062
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216144
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: 2.61→2.678 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 167 -
Rwork0.264 3327 -
obs-3327 99.94 %

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