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Yorodumi- PDB-1g7l: CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH ... -
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-Basic information
Entry | Database: PDB / ID: 1g7l | ||||||
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Title | CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME (HEL) COMPLEXED WITH THE MUTANT ANTI-HEL MONOCLONAL ANTIBODY D1.3 (VLW92S) | ||||||
Components |
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Keywords | HYDROLASE INHIBITOR/HYDROLASE / HYDROLASE INHIBITOR-HYDROLASE complex | ||||||
Function / homology | Function and homology information immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism ...immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / 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 | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Sundberg, E.J. / Urrutia, M. / Braden, B.C. / Isern, J. / Mariuzza, R.A. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface. Authors: Sundberg, E.J. / Urrutia, M. / Braden, B.C. / Isern, J. / Tsuchiya, D. / Fields, B.A. / Malchiodi, E.L. / Tormo, J. / Schwarz, F.P. / 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 | 1g7l.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g7l.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1g7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g7l ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g7l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 11601.845 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN / Mutation: W92S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 1333979 |
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#2: Antibody | Mass: 12857.275 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01820 |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
#4: 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: 2.37 Å3/Da / Density % sol: 48.09 % | |||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15-18% poly(ethylene glycol) 8000; 0.1 M potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||
Crystal grow | *PLUS Details: used macroseeding / PH range low: 6.5 / PH range high: 6 | |||||||||||||||
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: SIEMENS / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
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→99 Å / Num. all: 53007 / Num. obs: 23556 / % possible obs: 95.7 % / Rmerge(I) obs: 0.051 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 0.35 / % possible all: 93.1 |
Reflection | *PLUS Highest resolution: 2 Å / Num. measured all: 53007 |
Reflection shell | *PLUS % possible obs: 93.1 % / Rmerge(I) obs: 0.35 |
-Processing
Software |
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Refinement | Resolution: 2→15 Å
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / % reflection Rfree: 9.4 % / Rfactor obs: 0.207 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS |