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Yorodumi- PDB-3hfm: STRUCTURE OF AN ANTIBODY-ANTIGEN COMPLEX. CRYSTAL STRUCTURE OF TH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hfm | ||||||
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Title | STRUCTURE OF AN ANTIBODY-ANTIGEN COMPLEX. CRYSTAL STRUCTURE OF THE HY/HEL-10 FAB-LYSOZYME COMPLEX | ||||||
Components |
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Keywords | COMPLEX(ANTIBODY-ANTIGEN) | ||||||
Function / homology | Function and homology information 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 ...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: 3 Å | ||||||
Authors | Padlan, E.A. / Davies, D.R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1989 Title: Structure of an antibody-antigen complex: crystal structure of the HyHEL-10 Fab-lysozyme complex. Authors: Padlan, E.A. / Silverton, E.W. / Sheriff, S. / Cohen, G.H. / Smith-Gill, S.J. / Davies, D.R. #1: Journal: J.Mol.Biol. / Year: 1987 Title: A Three-Dimensional Model of an Anti-Lysozyme Antibody Authors: Smith-Gill, S.J. / Mainhart, C. / Lavoie, T.B. / Feldmann, R.J. / Drohan, W. / Brooks, B.R. #2: Journal: J.Mol.Biol. / Year: 1984 Title: Crystalline Monoclonal Antibody Fabs Complexed to Hen Egg White Lysozyme Authors: Silverton, E.W. / Padlan, E.A. / Davies, D.R. / Smith-Gill, S. / Potter, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hfm.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hfm.ent.gz | 90.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/3hfm ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hfm | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES PRO L 8, PRO L 95, PRO L 141, PRO H 147, PRO H 149 AND PRO H 187 ARE CIS-PROLINES. |
-Components
#1: Antibody | Mass: 23552.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
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#2: Antibody | Mass: 23322.873 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.93 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 180.761-765 1984 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 12501 / % possible obs: 78 % / Observed criterion σ(F): 3 / Rmerge(I) obs: 0.066 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 3→10 Å / Rfactor obs: 0.246 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.24 / Highest resolution: 3 Å / Lowest resolution: 10 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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