+Open data
-Basic information
Entry | Database: PDB / ID: 1dqm | ||||||
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Title | CRYSTAL STRUCTURE OF ANTI-LYSOZYME ANTIBODY | ||||||
Components |
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Keywords | IMMUNE SYSTEM / antibody / hen egg white lysozyme | ||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / B cell differentiation / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dqm.cif.gz | 100.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dqm.ent.gz | 79 KB | Display | PDB format |
PDBx/mmJSON format | 1dqm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dqm_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 1dqm_full_validation.pdf.gz | 446.8 KB | Display | |
Data in XML | 1dqm_validation.xml.gz | 22 KB | Display | |
Data in CIF | 1dqm_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/1dqm ftp://data.pdbj.org/pub/pdb/validation_reports/dq/1dqm | HTTPS FTP |
-Related structure data
-Links
-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. |
-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.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 2950241, UniProt: P01837*PLUS |
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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.) 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 |
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
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 |
-Processing
Software |
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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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