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Yorodumi- PDB-2iff: STRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX: EFFECT OF A CONSERVATI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2iff | ||||||
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Title | STRUCTURE OF AN ANTIBODY-LYSOZYME COMPLEX: EFFECT OF A CONSERVATIVE MUTATION | ||||||
Components |
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Keywords | IMMUNOGLOBULIN/HYDROLASE(O-GLYCOSYL) / IMMUNOGLOBULIN-HYDROLASE(O-GLYCOSYL) complex | ||||||
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: 2.65 Å | ||||||
Authors | Chacko, S. / Davies, D.R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Structure of an antibody-lysozyme complex unexpected effect of conservative mutation. Authors: Chacko, S. / Silverton, E. / Kam-Morgan, L. / Smith-Gill, S. / Cohen, G. / Davies, D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Three-Dimensional Structure of an Antibody-Antigen Complex Authors: Sheriff, S. / Silverton, E.W. / Padlan, E.A. / Cohen, G.H. / Smith-Gill, S.J. / Finzel, B.C. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2iff.cif.gz | 116.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2iff.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 2iff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/if/2iff ftp://data.pdbj.org/pub/pdb/validation_reports/if/2iff | 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: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 139 / 3: CIS PROLINE - PRO H 150 / 4: CIS PROLINE - PRO H 152 / 5: CIS PROLINE - PRO H 192 |
-Components
#1: Antibody | Mass: 23326.729 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1042224 |
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#2: Antibody | Mass: 22975.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) |
#3: Protein | Mass: 14303.146 Da / Num. of mol.: 1 / Mutation: R68K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00698 |
#4: Water | ChemComp-HOH / |
Sequence details | THE LIGHT CHAIN OF THE FAB HAS CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS CHAIN INDICATOR H. ...THE LIGHT CHAIN OF THE FAB HAS CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS CHAIN INDICATOR H. THE LYSOZYME HAS CHAIN INDICATOR Y. THE NUMBERING SYSTEM USED IN THIS ENTRY IS SEQUENTIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.97 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 9999 Å / Num. obs: 12909 / % possible obs: 66.4 % / Num. measured all: 37251 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / Lowest resolution: 2.76 Å / % possible obs: 22.3 % / Num. unique obs: 717 / Num. measured obs: 1140 / Mean I/σ(I) obs: 3.82 |
-Processing
Software |
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Refinement | Resolution: 2.65→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.183 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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