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- PDB-1j1x: Crystal Structure of HyHEL-10 Fv mutant LS93A complexed with hen ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j1x | ||||||
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Title | Crystal Structure of HyHEL-10 Fv mutant LS93A complexed with hen egg white lysozyme | ||||||
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![]() | IMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / IMMUNE SYSTEM-HYDROLASE COMPLEX | ||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / antigen binding / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...immunoglobulin complex / immunoglobulin mediated immune response / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / antigen binding / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / adaptive immune response / killing of cells of another organism / 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 | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yokota, A. / Tsumoto, K. / Shiroishi, M. / Kondo, H. / Kumagai, I. | ||||||
![]() | ![]() Title: The Role of Hydrogen Bonding via Interfacial Water Molecules in Antigen-Antibody Complexation. THE HyHEL-10-HEL INTERACTION Authors: Yokota, A. / Tsumoto, K. / Shiroishi, M. / Kondo, H. / Kumagai, I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 86.7 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11607.810 Da / Num. of mol.: 1 / Mutation: S93A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.2 % | ||||||||||||||||||||||||||||||
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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 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1999) J.Biol.Chem., 274, 27623. / PH range low: 7.8 / PH range high: 7.6 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2000 |
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→28.9 Å / Num. all: 36688 / Num. obs: 36671 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Rmerge(I) obs: 0.067 / Rsym value: 0.064 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5213 / Rsym value: 0.151 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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→1.82 Å
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Refinement | *PLUS Rfactor Rfree: 0.217 / Rfactor Rwork: 0.189 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_bond_d / Dev ideal: 0.004468 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.8 Å |