+Open data
-Basic information
Entry | Database: PDB / ID: 1jtp | ||||||
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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 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 | Camelus dromedarius (Arabian camel) Meleagris gallopavo (turkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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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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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jtp.cif.gz | 120.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jtp.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jtp_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 1jtp_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 1jtp_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 1jtp_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jtp ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jtp | HTTPS FTP |
-Related structure data
Related structure data | 1jtoC 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: 15757.232 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: 14228.105 Da / Num. of mol.: 2 / Fragment: ENZYME / Source method: isolated from a natural source / Details: Purchased from Sigma / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P00703, lysozyme #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-FMT / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98089 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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