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- PDB-4w81: Periplasmically Produced Monomeric Single Domain Antibody (sdAb) ... -

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Basic information

Entry
Database: PDB / ID: 4w81
TitlePeriplasmically Produced Monomeric Single Domain Antibody (sdAb) C22A/C99V variant against Staphylococcal enterotoxin B (SEB) at pH 8.0
ComponentsSingle Domain Antibody
KeywordsIMMUNE SYSTEM / single domain antibody / v-set domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGeorge, J. / Legler, 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
DepositionAug 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Derived calculations
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / 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_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Sep 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.number_atoms_total / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5202
Polymers15,4241
Non-polymers961
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.499, 87.499, 46.787
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Antibody Single Domain Antibody


Mass: 15424.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pet22 / Details (production host): Periplasmic / Production host: Escherichia coli (E. coli)
#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.: 52 / 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 REFERENCE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.74 % / Description: Three-sided pyramid
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Hampton Ammonium Sulfate Grid Screen condition B5 0.1 M Tris pH 8.0, 1.6 M Ammonium Sulfate

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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: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→43.75 Å / Num. obs: 6314 / % possible obs: 99.5 % / Redundancy: 5.37 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.1301 / Rsym value: 0.1 / Net I/σ(I): 10.6
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.4212 / Mean I/σ(I) obs: 3.19 / % possible all: 95.9

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W70

4w70


Resolution: 2.25→43.75 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.149 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.336 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23263 295 4.7 %RANDOM
Rwork0.19292 ---
obs0.19477 6017 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.521 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å2-0.42 Å20 Å2
2---0.84 Å2-0 Å2
3---1.25 Å2
Refinement stepCycle: 1 / Resolution: 2.25→43.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms993 0 5 52 1050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191017
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9831.941378
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4065130
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67623.11145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30515157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.618158
X-RAY DIFFRACTIONr_chiral_restr0.0640.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02783
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: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 28 -
Rwork0.23 426 -
obs--93.8 %

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