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- PDB-4tyu: Homodimeric Single Domain Antibody (sdAb) against Staphylococcal ... -

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Basic information

Entry
Database: PDB / ID: 4tyu
TitleHomodimeric Single Domain Antibody (sdAb) against Staphylococcal enterotoxin B (SEB)
ComponentsSingle Domain Antibody
KeywordsIMMUNE SYSTEM / Single domain antibody / camelid / v-set domain / amyloid like
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLegler, P.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Defense Threat Reduction Agency (DTRA)CBCALL12-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
DepositionJul 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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

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Assembly

Deposited unit
A: Single Domain Antibody
B: Single Domain Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0625
Polymers28,7742
Non-polymers2883
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-41 kcal/mol
Surface area12060 Å2
MethodPISA
2
A: Single Domain Antibody
B: Single Domain Antibody
hetero molecules

A: Single Domain Antibody
B: Single Domain Antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,12510
Polymers57,5484
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area5810 Å2
ΔGint-103 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.300, 72.240, 116.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21B-310-

HOH

31B-313-

HOH

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Components

#1: Antibody Single Domain Antibody


Mass: 14387.058 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pet15b / Details (production host): A3cytoWT / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.89 % / Description: rod-shaped
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.1 M citric acid pH 4.1, 1.6 M ammonium sulfate, 20 % glycerol
PH range: 4.1

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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 Platinum 135 / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: Bruker Helios Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.12→49.13 Å / Num. all: 16298 / Num. obs: 15098 / % possible obs: 92.6 % / Redundancy: 6.45 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.1387 / Rsym value: 0.088 / Net I/σ(I): 12.74
Reflection shellResolution: 2.12→2.22 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.3649 / Mean I/σ(I) obs: 4.88 / % possible all: 60.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PROTEUM PLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DKA

4dka


Resolution: 2.13→45.33 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.858 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26316 768 5.1 %RANDOM
Rwork0.23895 ---
obs0.2402 14319 92.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.374 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.13→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1978 0 15 75 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022028
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9442746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9185258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55623.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3421516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021558
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: 2.128→2.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 31 -
Rwork0.299 644 -
obs--57.3 %

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