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- PDB-4nc0: Crystal Structure of TcdA-A2 Bound to A26.8 VHH -

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Basic information

Entry
Database: PDB / ID: 4nc0
TitleCrystal Structure of TcdA-A2 Bound to A26.8 VHH
Components
  • 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: 2.3 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

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Assembly

Deposited unit
A: Cell wall-binding repeat protein
B: A26.8 VHH


Theoretical massNumber of molelcules
Total (without water)43,6532
Polymers43,6532
Non-polymers00
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.717, 117.802, 102.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

#1: Protein Cell wall-binding repeat protein


Mass: 29060.195 Da / Num. of mol.: 1 / 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 A26.8 VHH


Mass: 14593.076 Da / Num. of mol.: 1
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.: 210 / 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: 3.93 Å3/Da / Density % sol: 68.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.65 M Ammonium sulfate, 0.25 M Sodium chloride, 6% (w/v) glycerol, 0.1 M Sodium cacodylate, pH 6.5, 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: Jan 5, 2011 / 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: 2.3→40 Å / Num. all: 31316 / Num. obs: 31316 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 23.1
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 5.2 / Num. unique all: 2284 / Rsym value: 0.467 / % possible all: 100

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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 2G7C

2g7c


Resolution: 2.3→39.27 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.653 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.199 / ESU R Free: 0.169 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2234 1567 5 %RANDOM
Rwork0.19938 ---
obs0.20058 29831 99.93 %-
all-29831 --
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: 45.907 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20 Å20 Å2
2--3.07 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2922 0 0 210 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023001
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11.9154066
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24323.727161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25615446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8611518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212398
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 138 -
Rwork0.223 2133 -
obs--100 %

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