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- PDB-6e9g: The crystal structure of bovine ultralong antibody BOV-2 -

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Basic information

Entry
Database: PDB / ID: 6e9g
TitleThe crystal structure of bovine ultralong antibody BOV-2
Components
  • Bovine ultralong antibody BOV-2 heavy chain
  • Bovine ultralong antibody BOV-2 light chain
KeywordsIMMUNE SYSTEM / B-lymphocytes / antigen-antibody reactions / antibodies / monoclonal / antibody diversity / Bos taurus
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.904 Å
AuthorsDong, J. / Crowe, J.E.
CitationJournal: Front Immunol / Year: 2019
Title: Structural Diversity of Ultralong CDRH3s in Seven Bovine Antibody Heavy Chains.
Authors: Dong, J. / Finn, J.A. / Larsen, P.A. / Smith, T.P.L. / Crowe Jr., J.E.
History
DepositionAug 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bovine ultralong antibody BOV-2 heavy chain
B: Bovine ultralong antibody BOV-2 light chain


Theoretical massNumber of molelcules
Total (without water)51,4942
Polymers51,4942
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-32 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.366, 71.926, 88.004
Angle α, β, γ (deg.)90.00, 96.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Bovine ultralong antibody BOV-2 heavy chain


Mass: 28944.236 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#2: Antibody Bovine ultralong antibody BOV-2 light chain


Mass: 22549.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q3T101
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 10% PEG 200, 0.1 M Bis-Tris propane pH 9.0-9.5, 17% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.9→47.59 Å / Num. obs: 11347 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.6
Reflection shellResolution: 2.9→3.06 Å / Rmerge(I) obs: 0.23 / Num. unique all: 1586

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.904→47.59 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 603 5.32 %
Rwork0.2204 --
obs0.2227 11342 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.904→47.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3201 0 0 0 3201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023279
X-RAY DIFFRACTIONf_angle_d0.5814497
X-RAY DIFFRACTIONf_dihedral_angle_d7.611914
X-RAY DIFFRACTIONf_chiral_restr0.042523
X-RAY DIFFRACTIONf_plane_restr0.004578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9039-3.1960.34431420.2832618X-RAY DIFFRACTION98
3.196-3.65840.28751660.24822670X-RAY DIFFRACTION100
3.6584-4.60860.23321460.20462707X-RAY DIFFRACTION100
4.6086-47.59650.25391490.20672744X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 221.8821 Å / Origin y: 294.3749 Å / Origin z: 193.318 Å
111213212223313233
T0.3816 Å2-0.037 Å20.0063 Å2-0.3343 Å20.0673 Å2--0.5529 Å2
L2.1679 °2-0.2343 °21.779 °2-0.9645 °20.1299 °2--2.5595 °2
S-0.1007 Å °-0.4236 Å °0.0169 Å °0.0966 Å °0.1014 Å °0.0418 Å °-0.1755 Å °-0.0896 Å °0.0277 Å °
Refinement TLS groupSelection details: all

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