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Yorodumi- PDB-3a67: Crystal Structure of HyHEL-10 Fv mutant LN31D complexed with hen ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a67 | ||||||
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Title | Crystal Structure of HyHEL-10 Fv mutant LN31D complexed with hen egg white lysozyme | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / MUTANT / IMMUNE SYSTEM-HYDROLASE COMPLEX / Allergen / Antimicrobial / Bacteriolytic enzyme / Disulfide bond / Glycosidase | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Yokota, A. / Tsumoto, K. / Shiroishi, M. / Nakanishi, T. / Kondo, H. / Kumagai, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme Authors: Yokota, A. / Tsumoto, K. / Shiroishi, M. / Nakanishi, T. / Kondo, H. / Kumagai, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a67.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a67.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 3a67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/3a67 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/3a67 | HTTPS FTP |
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-Related structure data
Related structure data | 3a6bC 3a6cC 1c08S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 11624.795 Da / Num. of mol.: 1 / Mutation: N31D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKTN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
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#2: Antibody | Mass: 12795.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pKTN2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS ...THE SEQUENCE FOR CHAIN H IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS BELIEVE THAT ALA114 IS CORRECT. CHAIN L IS N31D MUTANT. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: PEG 6000, Hepes, glycerol, methyl-pentanediol, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30.434 Å / Num. all: 36664 / Num. obs: 36648 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 13.9 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 6.922 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 13 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5229 / Rsym value: 0.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C08 Resolution: 1.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1942976.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.6669 Å2 / ksol: 0.511146 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 21.75 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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