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Yorodumi- PDB-1xgt: Structure for antibody HyHEL-63 Y33L mutant complexed with hen eg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xgt | ||||||
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Title | Structure for antibody HyHEL-63 Y33L mutant complexed with hen egg lysozyme | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HyHel-63 / 2.1A crystal structure / Y33L mutant | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Li, Y. / Mariuzza, R.A. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Magnitude of the hydrophobic effect at central versus peripheral sites in protein-protein interfaces Authors: Li, Y. / Huang, Y. / Swaminathan, C.P. / Smith-Gill, S.J. / Mariuzza, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xgt.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xgt.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 1xgt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xgt_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 1xgt_full_validation.pdf.gz | 437.1 KB | Display | |
Data in XML | 1xgt_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 1xgt_validation.cif.gz | 37.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/1xgt ftp://data.pdbj.org/pub/pdb/validation_reports/xg/1xgt | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23715.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 22506.008 Da / Num. of mol.: 1 / Mutation: Y33L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
#3: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: P00698*PLUS, lysozyme |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.49 % |
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2→58.8 Å / Num. all: 42907 / Num. obs: 42907 / Biso Wilson estimate: 27.3 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→58.8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2338663.03 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 64.8158 Å2 / ksol: 0.41121 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→58.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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