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- PDB-2dqf: Crystal structure of hyhel-10 FV mutant (y33ay53a) complexed with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2dqf | ||||||
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Title | Crystal structure of hyhel-10 FV mutant (y33ay53a) 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 / adaptive immune response / killing of cells of another organism / defense response to Gram-negative bacterium / 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 | ![]() | 146.3 KB | Display | ![]() |
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PDB format | ![]() | 115.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 495.3 KB | Display | |
Data in XML | ![]() | 30.1 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dqcC ![]() 2dqdC ![]() 2dqeC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 11623.810 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 12611.747 Da / Num. of mol.: 2 / Mutation: Y33A,Y53A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE FOR CHAIN B AND E IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS ...THE SEQUENCE FOR CHAIN B AND E IS FROM THE PRF DATABASE, ACCESSION CODE 1306354A. AND, THE AUTHORS BELIEVE THAT ALA114 IS CORRECT. CHAIN B AND E IS ALSO TYR33ALA, TYR53ALA MUTANT. | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: AMMONIUM SULFATE, PEG4000, SODIUM ACETATE, pH 4.60, 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: 2.5→37 Å / Num. obs: 29457 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1C08 Resolution: 2.5→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: 43.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.023
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