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- PDB-6e9k: The crystal structure of bovine ultralong antibody BOV-5 -

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Basic information

Entry
Database: PDB / ID: 6e9k
TitleThe crystal structure of bovine ultralong antibody BOV-5
Components
  • Bovine ultralong antibody BOV-5 heavy chain
  • IGL@ protein
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: 2.193 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 20, 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-5 heavy chain
B: IGL@ protein


Theoretical massNumber of molelcules
Total (without water)50,3192
Polymers50,3192
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-32 kcal/mol
Surface area21910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.018, 70.795, 73.857
Angle α, β, γ (deg.)90.00, 107.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Bovine ultralong antibody BOV-5 heavy chain


Mass: 27769.834 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 IGL@ protein


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.: 81 / 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 291.15 K / Method: evaporation / Details: 25% PEG 4000, 6% tacsimate, 0.1 M MES pH 6.0

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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 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.19→43.035 Å / Num. obs: 21489 / % possible obs: 94 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 13.5
Reflection shellResolution: 2.19→2.31 Å / Rmerge(I) obs: 0.428 / Num. unique all: 2221

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.193→43.035 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2641 946 4.41 %
Rwork0.2042 --
obs0.2066 21463 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.193→43.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3329 0 0 81 3410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033404
X-RAY DIFFRACTIONf_angle_d0.5624651
X-RAY DIFFRACTIONf_dihedral_angle_d7.4182012
X-RAY DIFFRACTIONf_chiral_restr0.046548
X-RAY DIFFRACTIONf_plane_restr0.003590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1931-2.30870.3243930.30582049X-RAY DIFFRACTION66
2.3087-2.45340.33441480.26882903X-RAY DIFFRACTION94
2.4534-2.64280.33241590.25833078X-RAY DIFFRACTION99
2.6428-2.90870.29371420.23813059X-RAY DIFFRACTION99
2.9087-3.32940.27911330.22853108X-RAY DIFFRACTION99
3.3294-4.19420.25491420.18463125X-RAY DIFFRACTION100
4.1942-43.04290.21711290.16953195X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.3316 Å / Origin y: -11.6763 Å / Origin z: -19.1963 Å
111213212223313233
T0.3252 Å20.0459 Å2-0.0346 Å2-0.3084 Å20.0253 Å2--0.3223 Å2
L0.8732 °20.4546 °2-0.7745 °2-0.6674 °2-0.1815 °2--1.3144 °2
S0.0158 Å °0.084 Å °0.0663 Å °-0.0482 Å °0.0349 Å °-0.0248 Å °-0.1072 Å °-0.0128 Å °-0.0556 Å °
Refinement TLS groupSelection details: all

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