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Open data
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Basic information
Entry | Database: PDB / ID: 1dqm | ||||||
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Title | CRYSTAL STRUCTURE OF ANTI-LYSOZYME ANTIBODY | ||||||
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![]() | IMMUNE SYSTEM / antibody / hen egg white lysozyme | ||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Li, H. / Mariuzza, R.A. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.2 KB | Display | ![]() |
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PDB format | ![]() | 79 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.4 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 22 KB | Display | |
Data in CIF | ![]() | 31.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a heterodimer composed of heavy and light chains. |
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Components
#1: Antibody | Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 22556.023 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % | ||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 5, 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: 2.1→100 Å / Num. all: 26702 / Num. obs: 88367 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.328 / % possible all: 67.3 |
Reflection | *PLUS Num. obs: 26702 / Num. measured all: 88367 |
Reflection shell | *PLUS % possible obs: 67.3 % / Mean I/σ(I) obs: 1.7 |
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Processing
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Refinement | Resolution: 2.1→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→100 Å
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Refine LS restraints |
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Software | *PLUS Name: 'CNS' / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.269 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 30.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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