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Yorodumi- PDB-1uac: Crystal Structure of HYHEL-10 FV MUTANT SFSF Complexed with TURKE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uac | ||||||
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Title | Crystal Structure of HYHEL-10 FV MUTANT SFSF Complexed with TURKEY WHITE LYSOZYME | ||||||
Components |
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Keywords | IMMUNE SYSTEM/HYDROLASE / ANTIGEN-ANTIBODY COMPLEX / HYHEL-10 / MUTANT / ANTI-LYSOZYME ANTIBODY / IMMUNE SYSTEM-HYDROLASE COMPLEX | ||||||
Function / homology | Function and homology information glycosaminoglycan binding / 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 / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Meleagris gallopavo (turkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kumagai, I. / Nishimiya, Y. / Kondo, H. / Tsumoto, K. | ||||||
Citation | Journal: J.BIOL.CHEM. / Year: 2003 Title: Structural consequences of target epitope-directed functional alteration of an antibody. The case of anti-hen lysozyme antibody, HyHEL-10 Authors: Kumagai, I. / Nishimiya, Y. / Kondo, H. / Tsumoto, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uac.cif.gz | 83 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uac.ent.gz | 62.7 KB | Display | PDB format |
PDBx/mmJSON format | 1uac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uac_validation.pdf.gz | 384.3 KB | Display | wwPDB validaton report |
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Full document | 1uac_full_validation.pdf.gz | 397.7 KB | Display | |
Data in XML | 1uac_validation.xml.gz | 10 KB | Display | |
Data in CIF | 1uac_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ua/1uac ftp://data.pdbj.org/pub/pdb/validation_reports/ua/1uac | 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: 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) / References: GenBank: 196585 |
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#2: Antibody | Mass: 12763.939 Da / Num. of mol.: 1 / Mutation: Y53S, S54F, Y58F 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) / References: PRF: 1306354A |
#3: Protein | Mass: 14228.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / Tissue: EGG WHITE / References: UniProt: P00703, lysozyme |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.74 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6 Details: PEG 4000, ETHYLENE GLYCOL, AMMONIUM ACETATE, TRI-SODIUM CITRATE DEHYDRATE, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Kondo, H., (1999) J. Biol. Chem., 274, 27623. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Oct 7, 1999 / Details: mirrors and monochromator |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 36020 / % possible obs: 96.7 % / Biso Wilson estimate: 16.655 Å2 / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2 / Num. unique all: 5256 / % possible all: 95.2 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 3.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→20 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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