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- PDB-8cif: Bovine naive ultralong antibody AbD08 collected at 293K -

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Basic information

Entry
Database: PDB / ID: 8cif
TitleBovine naive ultralong antibody AbD08 collected at 293K
Components
  • Heavy chain
  • Light chain
KeywordsIMMUNE SYSTEM / ultralong / immunoglobulin / naive
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsClarke, J.D. / 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: Iucrj / Year: 2023
Title: Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.
Authors: Mikolajek, H. / Sanchez-Weatherby, J. / Sandy, J. / Gildea, R.J. / Campeotto, I. / Cheruvara, H. / Clarke, J.D. / Foster, T. / Fujii, S. / Paulsen, I.T. / Shah, B.S. / Hough, M.A.
#1: Journal: To Be Published
Title: The impact of chain-exchange on bovine ultralong immunoglobulins.
Authors: Clarke, J.D. / Douangamath, A. / Mikolajek, H. / Nyagwange, J. / Mwangi, W. / Placido, M.B.D. / Owens, R.J. / Stuart, D.I. / Hammond, J.
History
DepositionFeb 9, 2023Deposition 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy chain
L: Light chain


Theoretical massNumber of molelcules
Total (without water)57,8892
Polymers57,8892
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.228, 71.585, 100.233
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9938.29
21.9938.29
31.9938.29
41.9938.29
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop8.50.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.09M Sodium fluoride 0.09M Sodium iodide 0.09M Sodium bromide
2932vapor diffusion, sitting drop8.50.1M 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
2933vapor diffusion, sitting drop8.50.1M 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
2934vapor diffusion, sitting drop8.50.1M Tris (base) 0.1M Bicine 12% (v/v) PEG 500 MME 6% (v/v) PEG 20000 0.15M Sodium chloride 0.1M Sodium formate 0.1M Ammonium Acetate 0.1M Sodium citrate tribasic dihydrate 0.1M Potassium sodium tartrate tetrahydrate 0.1M Sodium oxamate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
12931N
22932N
32933N
42934N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDIAMOND VMXi10.9795
SYNCHROTRONDIAMOND VMXi20.9795
SYNCHROTRONDIAMOND VMXi30.9795
SYNCHROTRONDIAMOND VMXi40.9795
Detector
TypeIDDetectorDateDetails
DECTRIS EIGER2 X 4M1PIXELDec 2, 2019130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam
DECTRIS EIGER2 X 4M2PIXELDec 2, 2019130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam
DECTRIS EIGER2 X 4M3PIXELDec 2, 2019130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam
DECTRIS EIGER2 X 4M4PIXELDec 2, 2019130x80 microrad aperture, horizontally and vertically focusing mirrors, 4xslits, variable microfocus beam
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double multilayer, double crystalSINGLE WAVELENGTHMx-ray1
2Double multilayer, double crystalSINGLE WAVELENGTHMx-ray2
3Double multilayer, double crystalSINGLE WAVELENGTHMx-ray3
4Double multilayer, double crystalSINGLE WAVELENGTHMx-ray4
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
21
31
41
Reflection

Entry-ID: 8CIF / CC1/2: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.43-47.71478782.42.20.19713.5
2.07-58.2721940761.90.10326
2.17-58.232249146.51.80.11745.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
2.43-2.471.2270.47580.31
2.07-2.110.8310.56190.52
2.17-2.211.4050.57570.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS3.6.0-2-g5baae39f5-releasedata scaling
DIALS3.6.0-2-g5baae39f5-releasedata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58.32 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.338 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.269 / ESU R Free: 0.207
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22786 1127 4.9 %RANDOM
Rwork0.17713 ---
obs0.17963 21885 95.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.2→58.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 0 52 3467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133543
X-RAY DIFFRACTIONr_bond_other_d0.0010.0143123
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.6424855
X-RAY DIFFRACTIONr_angle_other_deg1.31.5677264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2955479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73223.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89815526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5891511
X-RAY DIFFRACTIONr_chiral_restr0.0650.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02744
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_it3.0593.7961891
X-RAY DIFFRACTIONr_mcbond_other3.0473.7931890
X-RAY DIFFRACTIONr_mcangle_it4.6915.6582357
X-RAY DIFFRACTIONr_mcangle_other4.695.662358
X-RAY DIFFRACTIONr_scbond_it3.5644.1871652
X-RAY DIFFRACTIONr_scbond_other3.5554.1871652
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.466.1172492
X-RAY DIFFRACTIONr_long_range_B_refined7.67144.2833519
X-RAY DIFFRACTIONr_long_range_B_other7.66544.293519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 77 -
Rwork0.262 1494 -
obs--90.34 %

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