+Open data
-Basic information
Entry | Database: PDB / ID: 6e9u | ||||||
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Title | The crystal structure of bovine ultralong antibody BOV-7 | ||||||
Components |
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Keywords | IMMUNE 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 / Immunoglobulin subtype / Immunoglobulin / 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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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 species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.295 Å | ||||||
Authors | Dong, J. / Crowe, J.E. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e9u.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e9u.ent.gz | 155.8 KB | Display | PDB format |
PDBx/mmJSON format | 6e9u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e9u_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 6e9u_full_validation.pdf.gz | 440.1 KB | Display | |
Data in XML | 6e9u_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 6e9u_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/6e9u ftp://data.pdbj.org/pub/pdb/validation_reports/e9/6e9u | HTTPS FTP |
-Related structure data
Related structure data | 6e8vC 6e9gC 6e9hC 6e9iC 6e9kC 6e9qC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 28976.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Homo sapiens (human) |
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#2: Antibody | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 291.15 K / Method: evaporation Details: 7% PEG 8000, 14% isopropanol, 0.1 M Tris-HCl pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.29→2.42 Å / Rmerge(I) obs: 0.33 / Num. unique all: 3106 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.295→40.77 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -10.6742 Å / Origin y: -10.6332 Å / Origin z: -19.8494 Å
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Refinement TLS group | Selection details: all |