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- PDB-6e9i: The crystal structure of bovine ultralong antibody BOV-4 -

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Basic information

Entry
Database: PDB / ID: 6e9i
TitleThe crystal structure of bovine ultralong antibody BOV-4
Components
  • Bovine ultralong antibody BOV-4 heavy chain
  • Bovine ultralong antibody BOV-4 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 / Immunoglobulin subtype / 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 / Immunoglobulin subtype / 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: 2.5 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 1.1May 8, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bovine ultralong antibody BOV-4 heavy chain
B: Bovine ultralong antibody BOV-4 light chain
C: Bovine ultralong antibody BOV-4 heavy chain
D: Bovine ultralong antibody BOV-4 light chain
H: Bovine ultralong antibody BOV-4 heavy chain
L: Bovine ultralong antibody BOV-4 light chain


Theoretical massNumber of molelcules
Total (without water)153,3946
Polymers153,3946
Non-polymers00
Water5,891327
1
A: Bovine ultralong antibody BOV-4 heavy chain
B: Bovine ultralong antibody BOV-4 light chain


Theoretical massNumber of molelcules
Total (without water)51,1312
Polymers51,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-32 kcal/mol
Surface area22970 Å2
MethodPISA
2
C: Bovine ultralong antibody BOV-4 heavy chain
D: Bovine ultralong antibody BOV-4 light chain


Theoretical massNumber of molelcules
Total (without water)51,1312
Polymers51,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-32 kcal/mol
Surface area22310 Å2
MethodPISA
3
H: Bovine ultralong antibody BOV-4 heavy chain
L: Bovine ultralong antibody BOV-4 light chain


Theoretical massNumber of molelcules
Total (without water)51,1312
Polymers51,1312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)148.547, 148.547, 165.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Antibody Bovine ultralong antibody BOV-4 heavy chain


Mass: 28581.701 Da / Num. of mol.: 3
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-4 light chain


Mass: 22549.596 Da / Num. of mol.: 3
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 / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 293.15 K / Method: evaporation
Details: 30% PEG 1000, 0.1 M sodium malonate pH 8.0, 0.1 M Tris-HCl pH 8.0

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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: Jul 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.5→46.65 Å / Num. obs: 66205 / % possible obs: 90.1 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 20.3
Reflection shellResolution: 2.5→2.64 Å / Rmerge(I) obs: 0.456 / Num. unique all: 9588

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→41.867 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 3357 5.08 %
Rwork0.2024 --
obs0.2044 66135 90.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→41.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10392 0 0 327 10719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310636
X-RAY DIFFRACTIONf_angle_d0.59714521
X-RAY DIFFRACTIONf_dihedral_angle_d8.6726284
X-RAY DIFFRACTIONf_chiral_restr0.0431683
X-RAY DIFFRACTIONf_plane_restr0.0041842
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53570.37271290.29252602X-RAY DIFFRACTION91
2.5357-2.57360.36181430.28682613X-RAY DIFFRACTION91
2.5736-2.61380.36661570.28322555X-RAY DIFFRACTION90
2.6138-2.65660.29831240.27132612X-RAY DIFFRACTION90
2.6566-2.70240.34831260.25322607X-RAY DIFFRACTION90
2.7024-2.75160.29771460.24612575X-RAY DIFFRACTION90
2.7516-2.80450.32741610.26362569X-RAY DIFFRACTION90
2.8045-2.86170.31511480.25252587X-RAY DIFFRACTION90
2.8617-2.92390.28561550.2592573X-RAY DIFFRACTION90
2.9239-2.99190.3371220.26292593X-RAY DIFFRACTION90
2.9919-3.06670.34081210.26532618X-RAY DIFFRACTION90
3.0667-3.14960.30051240.25622628X-RAY DIFFRACTION90
3.1496-3.24230.30451550.24892567X-RAY DIFFRACTION90
3.2423-3.34690.24261460.22892595X-RAY DIFFRACTION90
3.3469-3.46640.30911140.21962672X-RAY DIFFRACTION91
3.4664-3.60510.24131490.20972598X-RAY DIFFRACTION90
3.6051-3.76910.20991430.19942646X-RAY DIFFRACTION91
3.7691-3.96770.23931470.18542608X-RAY DIFFRACTION91
3.9677-4.21610.18941280.16892668X-RAY DIFFRACTION91
4.2161-4.54120.19491550.15172631X-RAY DIFFRACTION91
4.5412-4.99760.1721550.14442647X-RAY DIFFRACTION91
4.9976-5.71920.21831410.16052658X-RAY DIFFRACTION90
5.7192-7.19960.21321420.18282662X-RAY DIFFRACTION90
7.1996-41.87260.17641260.16752694X-RAY DIFFRACTION87
Refinement TLS params.Method: refined / Origin x: 21.2497 Å / Origin y: -44.1533 Å / Origin z: 19.1446 Å
111213212223313233
T0.3137 Å20.0427 Å20.0044 Å2-0.4038 Å20.0714 Å2--0.3919 Å2
L-0.0833 °2-0.0772 °20.1447 °2-0.5469 °2-0.4037 °2--0.4503 °2
S-0.0749 Å °-0.0071 Å °0.0203 Å °0.1715 Å °-0.0432 Å °-0.1346 Å °-0.1105 Å °0.1135 Å °0.0874 Å °
Refinement TLS groupSelection details: all

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