+Open data
-Basic information
Entry | Database: PDB / ID: 1jto | ||||||
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Title | Degenerate interfaces in antigen-antibody complexes | ||||||
Components |
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Keywords | Antibody / Hydrolase / immunoglobulin / heavy chain antibody / VHH / interface | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Camelus dromedarius (Arabian camel) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2001 Title: Degenerate interfaces in antigen-antibody complexes. Authors: Decanniere, K. / Transue, T.R. / Desmyter, A. / Maes, D. / Muyldermans, S. / Wyns, L. #1: Journal: Nat.Struct.Biol. / Year: 1996 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jto.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jto.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jto ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jto | HTTPS FTP |
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-Related structure data
Related structure data | 1jtpC 1jttC 1melS S: Starting model for refinement 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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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.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN1 / Production host: Escherichia coli (E. coli) / References: GenBank: 2392447 #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) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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