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Open data
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Basic information
Entry | Database: PDB / ID: 1jto | ||||||
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Title | Degenerate interfaces in antigen-antibody complexes | ||||||
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![]() | Antibody / Hydrolase / immunoglobulin / heavy chain antibody / VHH / interface | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L. | ||||||
![]() | ![]() Title: Degenerate interfaces in antigen-antibody complexes. Authors: Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L. #1: ![]() Title: Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme Authors: Desmyter, A. / Transue, T.R. / Ghahroudi, M.A. / Thi, M.H. / Poortmans, F. / Hamers, R. / Muyldermans, S. / Wyns, L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 108.7 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jtpC ![]() 1jttC ![]() 1melS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 15657.090 Da / Num. of mol.: 2 / Fragment: VH domain fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Fragment: Enzyme / Source method: isolated from a natural source / Details: Purchased from Sigma / Source: (natural) ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.77 % | |||||||||||||||
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG 8000, potassium phosphate, , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 300K | |||||||||||||||
Crystal grow | *PLUS pH: 5.6 / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1996 |
Radiation | Monochromator: Graphite single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 17829 / Num. obs: 17829 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. unique all: 1170 / Rsym value: 0.42 / % possible all: 84.8 |
Reflection | *PLUS |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MEL Resolution: 2.5→20 Å / Isotropic thermal model: Overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.173 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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