[English] 日本語
Yorodumi- PDB-2dqj: Crystal structure of hyhel-10 FV (wild-type) complexed with hen e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hyhel-10 FV (wild-type) complexed with hen egg lysozyme at 1.8A resolution | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / IMMUNE SYSTEM-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Shiroishi, M. / Kondo, H. / Tsumoto, K. / Kumagai, I. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 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. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2dqj.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2dqj.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqj ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqj | HTTPS FTP |
---|
-Related structure data
Related structure data | 2dqcC 2dqdC 2dqeC 2dqfC 2dqgC 2dqhC 2dqiC 1c08S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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) / Plasmid: PKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
---|---|
#2: Antibody | Mass: 12795.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PKTN2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme |
#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. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.93 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: HEPES, MPD, PEG6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / 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: 1.8→28.7 Å / Num. obs: 36103 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 7 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 4.3 / % possible all: 98.8 |
-Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1C08 Resolution: 1.8→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| ||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.82 Å
|