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- PDB-6e9u: The crystal structure of bovine ultralong antibody BOV-7 -

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Basic information

Entry
Database: PDB / ID: 6e9u
TitleThe crystal structure of bovine ultralong antibody BOV-7
Components
  • Bovine ultralong antibody BOV-7 heavy chain
  • Bovine ultralong antibody BOV-7 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: 2.295 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 13, 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-7 heavy chain
B: Bovine ultralong antibody BOV-7 light chain


Theoretical massNumber of molelcules
Total (without water)51,5262
Polymers51,5262
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-33 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.261, 79.245, 62.164
Angle α, β, γ (deg.)90.00, 95.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Bovine ultralong antibody BOV-7 heavy chain


Mass: 28976.062 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-7 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 291.15 K / Method: evaporation
Details: 7% PEG 8000, 14% isopropanol, 0.1 M Tris-HCl pH 7.5

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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: Feb 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.29→48.79 Å / Num. obs: 21713 / % possible obs: 99.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.4
Reflection shellResolution: 2.29→2.42 Å / Rmerge(I) obs: 0.33 / Num. unique all: 3106

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Processing

Software
NameVersionClassification
PHENIX(1.14_3211: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.295→40.77 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2565 1062 4.9 %
Rwork0.2138 --
obs0.2159 21686 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.295→40.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3480 0 0 116 3596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023566
X-RAY DIFFRACTIONf_angle_d0.5544873
X-RAY DIFFRACTIONf_dihedral_angle_d8.2352092
X-RAY DIFFRACTIONf_chiral_restr0.042559
X-RAY DIFFRACTIONf_plane_restr0.004620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2946-2.3990.30821430.28452534X-RAY DIFFRACTION98
2.399-2.52550.33391030.28632579X-RAY DIFFRACTION99
2.5255-2.68370.3691330.28672549X-RAY DIFFRACTION100
2.6837-2.89080.2791250.26782572X-RAY DIFFRACTION100
2.8908-3.18160.31961420.25792586X-RAY DIFFRACTION100
3.1816-3.64180.29231280.22742603X-RAY DIFFRACTION100
3.6418-4.58720.23981430.18222591X-RAY DIFFRACTION100
4.5872-40.77680.17821450.1632610X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.6742 Å / Origin y: -10.6332 Å / Origin z: -19.8494 Å
111213212223313233
T0.2593 Å20.008 Å2-0.0311 Å2-0.2282 Å2-0.066 Å2--0.4131 Å2
L0.7917 °2-0.1329 °2-0.1826 °2-0.1422 °2-0.1804 °2--4.3794 °2
S0.1335 Å °-0.0796 Å °0.0728 Å °-0.0426 Å °0.0492 Å °0.0381 Å °0.1288 Å °0.2922 Å °-0.1566 Å °
Refinement TLS groupSelection details: all

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