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- PDB-6e8v: The crystal structure of bovine ultralong antibody BOV-1 -

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Basic information

Entry
Database: PDB / ID: 6e8v
TitleThe crystal structure of bovine ultralong antibody BOV-1
Components
  • Bovine ultralong antibody BOV-1 Heavy chain
  • Bovine ultralong antibody BOV-1 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 C1-set domain ...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: 3.79 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
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2020Group: Data collection / Category: reflns_shell / Item: _reflns_shell.Rmerge_I_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bovine ultralong antibody BOV-1 Heavy chain
B: Bovine ultralong antibody BOV-1 light chain
E: Bovine ultralong antibody BOV-1 Heavy chain
F: Bovine ultralong antibody BOV-1 light chain
H: Bovine ultralong antibody BOV-1 Heavy chain
J: Bovine ultralong antibody BOV-1 Heavy chain
K: Bovine ultralong antibody BOV-1 light chain
L: Bovine ultralong antibody BOV-1 light chain
O: Bovine ultralong antibody BOV-1 Heavy chain
P: Bovine ultralong antibody BOV-1 light chain
U: Bovine ultralong antibody BOV-1 Heavy chain
V: Bovine ultralong antibody BOV-1 light chain
Y: Bovine ultralong antibody BOV-1 Heavy chain
Z: Bovine ultralong antibody BOV-1 light chain
c: Bovine ultralong antibody BOV-1 Heavy chain
d: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)408,83416
Polymers408,83416
Non-polymers00
Water0
1
A: Bovine ultralong antibody BOV-1 Heavy chain
B: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-30 kcal/mol
Surface area19470 Å2
MethodPISA
2
E: Bovine ultralong antibody BOV-1 Heavy chain
F: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-28 kcal/mol
Surface area21840 Å2
MethodPISA
3
H: Bovine ultralong antibody BOV-1 Heavy chain
L: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-29 kcal/mol
Surface area21770 Å2
MethodPISA
4
J: Bovine ultralong antibody BOV-1 Heavy chain
K: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-32 kcal/mol
Surface area19830 Å2
MethodPISA
5
O: Bovine ultralong antibody BOV-1 Heavy chain
P: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area19560 Å2
MethodPISA
6
U: Bovine ultralong antibody BOV-1 Heavy chain
V: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-29 kcal/mol
Surface area21940 Å2
MethodPISA
7
Y: Bovine ultralong antibody BOV-1 Heavy chain
Z: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-29 kcal/mol
Surface area19940 Å2
MethodPISA
8
c: Bovine ultralong antibody BOV-1 Heavy chain
d: Bovine ultralong antibody BOV-1 light chain


Theoretical massNumber of molelcules
Total (without water)51,1042
Polymers51,1042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-28 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)308.219, 308.219, 133.752
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Antibody
Bovine ultralong antibody BOV-1 Heavy chain


Mass: 28554.646 Da / Num. of mol.: 8
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-1 light chain


Mass: 22549.596 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: IGL@ / Production host: Homo sapiens (human) / References: UniProt: Q3T101

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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: 4.15 Å3/Da / Density % sol: 70.36 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 14-18% PEG 3350, 0.1 M Citric acid pH 4.0-45., 0.1 M sodium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.196→49.84 Å / Num. obs: 89101 / % possible obs: 100 % / Redundancy: 7.5 %
Data reduction details: The data is highly anisotropic. The diffraction anisotropy server at UCLA was used to anisotropically scale the data to 3.20 angstrom along a*, b* axes, and to 3.80 angstrom along c* axis
Rmerge(I) obs: 0.216 / Net I/σ(I): 8.5
Reflection shellResolution: 3.196→3.2318 Å / Rmerge(I) obs: 1.44 / Num. unique all: 3534

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.79→49.203 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2745 3245 5.06 %
Rwork0.2183 --
obs0.2212 64076 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.79→49.203 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25749 0 0 0 25749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00426318
X-RAY DIFFRACTIONf_angle_d0.65435959
X-RAY DIFFRACTIONf_dihedral_angle_d7.14615466
X-RAY DIFFRACTIONf_chiral_restr0.0444248
X-RAY DIFFRACTIONf_plane_restr0.0054540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7901-3.84660.30871380.28092606X-RAY DIFFRACTION100
3.8466-3.90670.32271350.2882602X-RAY DIFFRACTION100
3.9067-3.97070.38851210.26772622X-RAY DIFFRACTION100
3.9707-4.03910.34281530.25832614X-RAY DIFFRACTION100
4.0391-4.11260.29911580.24362585X-RAY DIFFRACTION100
4.1126-4.19160.28651350.25312611X-RAY DIFFRACTION100
4.1916-4.27710.27311240.22032598X-RAY DIFFRACTION99
4.2771-4.37010.27281580.21262592X-RAY DIFFRACTION99
4.3701-4.47170.23951560.20072623X-RAY DIFFRACTION100
4.4717-4.58340.21481260.19832611X-RAY DIFFRACTION100
4.5834-4.70720.23441620.19542605X-RAY DIFFRACTION100
4.7072-4.84560.26981460.19312618X-RAY DIFFRACTION100
4.8456-5.00190.27491350.19442633X-RAY DIFFRACTION100
5.0019-5.18050.23721370.20082657X-RAY DIFFRACTION100
5.1805-5.38770.29881200.20472655X-RAY DIFFRACTION100
5.3877-5.63250.26431750.21772614X-RAY DIFFRACTION100
5.6325-5.9290.27291290.22452667X-RAY DIFFRACTION100
5.929-6.29980.31151310.22232667X-RAY DIFFRACTION100
6.2998-6.78510.26871540.22212664X-RAY DIFFRACTION100
6.7851-7.46580.27521260.22282716X-RAY DIFFRACTION100
7.4658-8.54120.25871430.20752697X-RAY DIFFRACTION100
8.5412-10.74250.23711490.18212735X-RAY DIFFRACTION100
10.7425-49.20680.32591340.23922839X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 57.6253 Å / Origin y: 209.4699 Å / Origin z: 274.5893 Å
111213212223313233
T0.6777 Å2-0.1155 Å2-0.0029 Å2-0.706 Å2-0.0041 Å2--1.1436 Å2
L0.037 °2-0.0783 °20.0033 °2-0.1776 °2-0.032 °2--0.3233 °2
S-0.0528 Å °0.0059 Å °-0.0483 Å °-0.0153 Å °-0.0186 Å °0.022 Å °0.0652 Å °-0.1014 Å °0.0604 Å °
Refinement TLS groupSelection details: all

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