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- PDB-4nby: Crystal Structure of TcdA-A2 Bound to Two Molecules of A20.1 VHH -

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Basic information

Entry
Database: PDB / ID: 4nby
TitleCrystal Structure of TcdA-A2 Bound to Two Molecules of A20.1 VHH
Components
  • A20.1 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: 2.08 Å
AuthorsMurase, T. / Eugenio, L. / Schorr, M. / Hussack, G. / Tanha, J. / Kitova, E. / 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 1.4Nov 6, 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: A20.1 VHH
C: A20.1 VHH


Theoretical massNumber of molelcules
Total (without water)63,2053
Polymers63,2053
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.390, 80.390, 410.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cell wall-binding repeat protein


Mass: 29547.760 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 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1 M Ammonium sulfate, 0.1 M Tris-Cl, pH 7.5, 0.1 M TMAO, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2012 / Details: mirrors
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.08→40 Å / Num. all: 48737 / Num. obs: 48737 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 23.4
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 5.2 / Num. unique all: 3513 / Rsym value: 0.692 / % 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: 2.08→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.121 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.17 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25465 2439 5 %RANDOM
Rwork0.20948 ---
obs0.21171 46333 99.9 %-
all-46333 --
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: 34.296 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20.67 Å20 Å2
2--0.67 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.08→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 0 408 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.023979
X-RAY DIFFRACTIONr_angle_refined_deg1.0841.9195396
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4723.596203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54915579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9641524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2540
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213179
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 175 -
Rwork0.241 3322 -
obs-3513 99.86 %

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