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- PDB-8bs8: Bovine naive ultralong antibody AbD08 collected at 100K -

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Basic information

Entry
Database: PDB / ID: 8bs8
TitleBovine naive ultralong antibody AbD08 collected at 100K
Components
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / ultralong / immunoglobulin / naive
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsClarke, J.D. / Douangamath, A. / Mikolajek, H. / Stuart, D.I. / Owens, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011224/1 United Kingdom
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2024
Title: The impact of exchanging the light and heavy chains on the structures of bovine ultralong antibodies.
Authors: Clarke, J.D. / Douangamath, A. / Mikolajek, H. / Bonnet-Di Placido, M. / Ren, J. / Fry, E.E. / Stuart, D.I. / Hammond, J.A. / Owens, R.J.
#1: Journal: To Be Published
Title: The impact of chain-exchange on bovine ultralong immunoglobulins
Authors: Clarke, J.D. / Douangamath, A. / Mikolajek, H. / Placido, M.D.P. / Owens, R.J. / Stuart, D.I. / Hammond, J.
History
DepositionNov 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain
L: Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0113
Polymers57,8892
Non-polymers1221
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-27 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 71.110, 98.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Heavy chain


Mass: 32569.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: PBMC / Cell: B lymphocyte / Plasmid: pOPINBOVH / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light chain


Mass: 25319.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Tissue: PBMC / Cell: B lymphocyte / Plasmid: pOPINBOVL / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12372351 Å3/Da / Density % sol: 42.1188431 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.09M Sodium nitrate 0.09M Sodium phosphate dibasic 0.09M Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2019
Details: 130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable focus beam
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→57.64 Å / Num. obs: 60610 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Rrim(I) all: 0.063 / Χ2: 0.98 / Net I/σ(I): 13.5 / Num. measured all: 408647
Reflection shellResolution: 1.59→1.62 Å / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 1.307 / Num. measured all: 20025 / Num. unique obs: 2943 / CC1/2: 0.62 / Rpim(I) all: 0.541 / Rrim(I) all: 1.416 / Χ2: 0.79 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
pointless1.11.21data scaling
xia20.6.277-g54103976-dials-2.0data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→57.64 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.301 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21889 3079 5.1 %RANDOM
Rwork0.1745 ---
obs0.17683 57461 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å2-0 Å2
2---0.67 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.59→57.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 8 590 4088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123641
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163136
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.6464984
X-RAY DIFFRACTIONr_angle_other_deg0.5161.5537367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.875496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.109512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80310524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.070.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02680
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_it1.9532.2321941
X-RAY DIFFRACTIONr_mcbond_other1.9322.2321941
X-RAY DIFFRACTIONr_mcangle_it2.8453.332418
X-RAY DIFFRACTIONr_mcangle_other2.8453.3312419
X-RAY DIFFRACTIONr_scbond_it2.5262.4061700
X-RAY DIFFRACTIONr_scbond_other2.5252.4061701
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6293.5152556
X-RAY DIFFRACTIONr_long_range_B_refined7.11143.7154120
X-RAY DIFFRACTIONr_long_range_B_other6.90136.7313931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 222 -
Rwork0.297 4157 -
obs--99.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3613-0.06250.03070.32540.26591.8599-0.0028-0.0745-0.02380.05910.00590.00420.0716-0.0617-0.00310.0119-0.0010.00680.01730.00920.071662.475656.69233.0573
20.426-0.1818-0.24030.12130.28522.52240.0252-0.0276-0.04190.0138-0.0111-0.0120.0563-0.1086-0.0140.0243-0.0125-0.0190.01690.02560.056768.637540.7301-6.7769
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H28 - 298
2X-RAY DIFFRACTION2L29 - 244

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