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- PDB-1ic4: CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ic4 | ||||||
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Title | CRYSTAL STRUCTURE OF HYHEL-10 FV MUTANT(HD32A)-HEN LYSOZYME COMPLEX | ||||||
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![]() | PROTEIN BINDING/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / HYHEL-10 / ANTI-HEN EGG WHITE LYSOZYME ANTIBODY / PROTEIN BINDING-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 | ![]() ![]() | ||||||
![]() | Shiroishi, M. / Yokota, A. / Tsumoto, K. / Kondo, H. / Nishimiya, Y. / Horii, K. / Matsushima, M. / Ogasahara, K. / Yutani, K. / Kumagai, I. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 76.4 KB | Display | ![]() |
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PDB format | ![]() | 61.8 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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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.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 12751.929 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-114 / Mutation: D32A 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: 2.51 Å3/Da / Density % sol: 50.94 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: HEPES, MPD, PEG6000, 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: ![]() |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Mar 16, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 74484 / Num. obs: 17573 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.508 / % possible all: 94.9 |
Reflection | *PLUS Num. measured all: 74484 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 96.1 % / Rmerge(I) obs: 0.318 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / σ(F): 0 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_angle_d / Dev ideal: 2.7 |