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Open data
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Basic information
Entry | Database: PDB / ID: 1jtp | ||||||
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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 | ![]() glycosaminoglycan binding / 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 / 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. | ||||||
History |
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Remark 999 | SEQUENCE ARG IS PART OF THE HEMAGLUTAMINE-TAG, WHILE THE ENTRY IN THE GB DATABASE REPRESENTS THE ...SEQUENCE ARG IS PART OF THE HEMAGLUTAMINE-TAG, WHILE THE ENTRY IN THE GB DATABASE REPRESENTS THE SAME MOLECULE WITH A HIS-TAG. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.3 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1jtoC ![]() 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: 15757.232 Da / Num. of mol.: 2 / Fragment: VH DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 14228.105 Da / Num. of mol.: 2 / Fragment: ENZYME / Source method: isolated from a natural source / Details: Purchased from Sigma / Source: (natural) ![]() ![]() #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.03 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2M Na Formate, 100mM Na Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1998 |
Radiation | Monochromator: 0.98089 Angstrom / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98089 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→17 Å / Num. all: 42348 / Num. obs: 40619 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2 / Num. unique all: 3873 / Rsym value: 0.417 / % possible all: 92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code: 1MEL Resolution: 1.9→17 Å / Isotropic thermal model: isotropic / Cross valid method: Free-R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Eng & Huber Details: overall anisotropic B-factor and bulk solvent correction used
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Displacement parameters | Biso mean: 20.38 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→17 Å
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