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Yorodumi- PDB-1ic7: CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ic7 | ||||||
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Title | CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A99A)-HEN LYSOZYME COMPLEX | ||||||
Components |
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Keywords | PROTEIN BINDING/HYDROLASE / antigen-antibody complex / HYHEL-10 / ANTI-HEN EGG WHITE LYSOZYME ANTIBODY / PROTEIN BINDING-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 / adaptive immune response / defense response to Gram-positive bacterium / defense response to bacterium / immune response / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Shiroishi, M. / Yokota, A. / Tsumoto, K. / Kondo, H. / Nishimiya, Y. / Horii, K. / Matsushima, M. / Ogasahara, K. / Yutani, K. / Kumagai, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Structural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex. Authors: Shiroishi, M. / Yokota, A. / Tsumoto, K. / Kondo, H. / Nishimiya, Y. / Horii, K. / Matsushima, M. / Ogasahara, K. / Yutani, K. / Kumagai, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ic7.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ic7.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 1ic7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/1ic7 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/1ic7 | 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: 11623.810 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01642 |
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#2: Antibody | Mass: 12707.919 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114 / Mutation: D32A/D99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01823 |
#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: 2.52 Å3/Da / Density % sol: 51.14 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: HEPES, PEG6000, MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS Method: unknown / PH range low: 7.8 / PH range high: 7.6 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 1, 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→20 Å / Num. all: 153223 / Num. obs: 23833 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.342 / % possible all: 98.9 |
Reflection | *PLUS Num. measured all: 153223 |
Reflection shell | *PLUS % possible obs: 98.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→8 Å / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor Rfree: 0.23 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |