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- PDB-2dqe: Crystal structure of hyhel-10 FV mutant (Hy53a) complexed with he... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dqe | ||||||
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Title | Crystal structure of hyhel-10 FV mutant (Hy53a) complexed with hen egg lysozyme | ||||||
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![]() | IMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / MUTANT / IMMUNE SYSTEM-HYDROLASE COMPLEX | ||||||
Function / homology | ![]() immunoglobulin complex / immunoglobulin mediated immune response / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / antigen binding / RNA-directed DNA polymerase activity / cell wall macromolecule catabolic process / lysozyme ...immunoglobulin complex / immunoglobulin mediated immune response / Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / antigen binding / RNA-directed DNA polymerase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / adaptive immune response / killing of cells of another organism / blood microparticle / 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. / Kondo, H. / Tsumoto, K. / Kumagai, I. | ||||||
![]() | ![]() Title: Structural consequences of mutations in interfacial Tyr residues of a protein antigen-antibody complex. The case of HyHEL-10-HEL Authors: Shiroishi, M. / Tsumoto, K. / Tanaka, Y. / Yokota, A. / Nakanishi, T. / Kondo, H. / Kumagai, I. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 64.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.9 KB | Display | ![]() |
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Full document | ![]() | 442.3 KB | Display | |
Data in XML | ![]() | 17.6 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dqcC ![]() 2dqdC ![]() 2dqfC ![]() 2dqgC ![]() 2dqhC ![]() 2dqiC ![]() 2dqjC ![]() 1c08S S: Starting model for refinement C: citing same article ( |
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Similar 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: 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: 12703.843 Da / Num. of mol.: 1 / Mutation: Y53A 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 / |
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 H IS ALSO TYR53ALA MUTANT. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 43.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HEPES, MPD, PEG6000, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 30841 / % possible obs: 99.8 % / Observed criterion σ(I): 1 / Redundancy: 14.1 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.6 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C08 Resolution: 1.9→8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016
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