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- PDB-4w68: Cytoplasmically Produced Homodimeric Single Domain Antibody (sdAb... -

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Basic information

Entry
Database: PDB / ID: 4w68
TitleCytoplasmically Produced Homodimeric Single Domain Antibody (sdAb) C22A/C99V variant against Staphylococcal enterotoxin B (SEB)
ComponentsSingle domain antibody
KeywordsIMMUNE SYSTEM / beta helical / amyloid-like / misfolded / dimeric
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGeorge, J. / Legler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CBCAL12-LS6-2-0036 United States
CitationJournal: Proteins / Year: 2014
Title: Structural and mutational analysis of a monomeric and dimeric form of a single domain antibody with implications for protein misfolding.
Authors: George, J. / Compton, J.R. / Leary, D.H. / Olson, M.A. / Legler, P.M.
History
DepositionAug 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Single domain antibody
A: Single domain antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7983
Polymers28,7022
Non-polymers961
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.893, 72.044, 116.103
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: Antibody Single domain antibody


Mass: 14350.981 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pet15b / Details (production host): Cytoplasmic / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSEQUENCE REFLECTS C22A, C99V MUTATIONS AGAINST WT PROTEIN. NO UNP MATCH IS FOUND, THEREFORE THE ...SEQUENCE REFLECTS C22A, C99V MUTATIONS AGAINST WT PROTEIN. NO UNP MATCH IS FOUND, THEREFORE THE SEQUENCE IS SELF REFERENCED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.47 % / Description: rod-shaped
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris pH 8.0, 1.6 M Ammonium Sulfate [Hampton Research Ammonium Sulfate Grid Screen, condition B5]

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Sep 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→58.05 Å / Num. obs: 18197 / % possible obs: 94.3 % / Redundancy: 10.57 % / Biso Wilson estimate: 15.3 Å2 / Rmerge(I) obs: 0.1038 / Rsym value: 0.054 / Net I/σ(I): 16.86
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.29 % / Rmerge(I) obs: 0.3556 / Mean I/σ(I) obs: 3.32 / % possible all: 71.8

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TYU

4tyu


Resolution: 2→58.05 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2422 945 5.2 %RANDOM
Rwork0.19914 ---
obs0.2013 17228 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0 Å2
2--1 Å20 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 2→58.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 5 103 2086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192020
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9392736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0515258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11523.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75315314
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.851516
X-RAY DIFFRACTIONr_chiral_restr0.080.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021558
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: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 52 -
Rwork0.245 926 -
obs--69.02 %

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