+Open data
-Basic information
Entry | Database: PDB / ID: 1dqq | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF ANTI-LYSOZYME ANTIBODY HYHEL-63 | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / anti-lysozyme antibody / HyHEL-63 / hen egg white lysozyme | ||||||
Function / homology | Function and homology information Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Li, H. / Mariuzza, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,). Authors: Li, Y. / Li, H. / Smith-Gill, S.J. / Mariuzza, R.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dqq.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dqq.ent.gz | 156.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqq ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqq | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a heterodimer composed of heavy and light chains. |
-Components
#1: Antibody | Mass: 23583.869 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 2950241, UniProt: P01837*PLUS #2: Antibody | Mass: 22556.023 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01863*PLUS #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.09 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 8000, KH2PO4, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal volume of protein and reservoir solutions | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jun 6, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→100 Å / Num. all: 68027 / Num. obs: 145275 / % possible obs: 86.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.02 / % possible all: 54.5 |
Reflection | *PLUS Num. obs: 68027 / Num. measured all: 145275 |
Reflection shell | *PLUS % possible obs: 54.5 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→100 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.7 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|