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- PDB-6e9h: The crystal structure of bovine ultralong antibody BOV-3 -

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Basic information

Entry
Database: PDB / ID: 6e9h
TitleThe crystal structure of bovine ultralong antibody BOV-3
Components
  • Bovine ultralong antibody BOV-3 heavy chain
  • Bovine ultralong antibody BOV-3 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.1Oct 30, 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-3 heavy chain
B: Bovine ultralong antibody BOV-3 light chain


Theoretical massNumber of molelcules
Total (without water)51,7622
Polymers51,7622
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-33 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.247, 71.219, 119.789
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 Bovine ultralong antibody BOV-3 heavy chain


Mass: 29212.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Homo sapiens (human)
#2: Antibody Bovine ultralong antibody BOV-3 light chain


Mass: 22549.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q3T101
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
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: 2.11 Å3/Da / Density % sol: 41.75 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 30% PEG 1000, 0.1 M sodium malonate pH 8.0, 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→47.12 Å / Num. obs: 30426 / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.224 / Num. unique all: 4354

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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→45.839 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 1482 4.88 %
Rwork0.217 --
obs0.2189 30350 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→45.839 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 0 201 3643
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023525
X-RAY DIFFRACTIONf_angle_d0.4934814
X-RAY DIFFRACTIONf_dihedral_angle_d2.162415
X-RAY DIFFRACTIONf_chiral_restr0.04559
X-RAY DIFFRACTIONf_plane_restr0.003610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.06460.35151280.28852590X-RAY DIFFRACTION100
2.0646-2.13830.31821160.28582615X-RAY DIFFRACTION100
2.1383-2.2240.32391390.28152558X-RAY DIFFRACTION100
2.224-2.32520.29851210.27562613X-RAY DIFFRACTION100
2.3252-2.44780.32741120.27092623X-RAY DIFFRACTION100
2.4478-2.60110.30511370.2812573X-RAY DIFFRACTION100
2.6011-2.80190.30991350.27052606X-RAY DIFFRACTION100
2.8019-3.08380.25131510.24722615X-RAY DIFFRACTION100
3.0838-3.52990.24851460.22452634X-RAY DIFFRACTION100
3.5299-4.44670.23841670.17982640X-RAY DIFFRACTION100
4.4467-45.85120.20061300.16162801X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.6266 Å / Origin y: 9.3363 Å / Origin z: 5.2391 Å
111213212223313233
T0.2692 Å20.0493 Å20.0312 Å2-0.2597 Å20.0188 Å2--0.3528 Å2
L0.483 °20.1417 °20.3533 °2-0.8202 °20.353 °2--2.2052 °2
S0.0414 Å °0.0701 Å °-0.0302 Å °0.0242 Å °-0.0157 Å °0.0495 Å °0.1293 Å °0.1623 Å °-0.0224 Å °
Refinement TLS groupSelection details: all

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