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Yorodumi- PDB-1kxx: ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1kxx | ||||||
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Title | ANALYSIS OF THE STABILIZATION OF HEN LYSOZYME WITH THE HELIX DIPOLE AND CHARGED SIDE CHAINS | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ELECTROSTATIC INTERACTION / HELIX / HEN LYSOZYME / STABILITY | ||||||
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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.71 Å | ||||||
Authors | Motoshima, H. / Ohmura, T. / Ueda, T. / Imoto, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 1997 Title: Analysis of the stabilization of hen lysozyme by helix macrodipole and charged side chain interaction. Authors: Motoshima, H. / Mine, S. / Masumoto, K. / Abe, Y. / Iwashita, H. / Hashimoto, Y. / Chijiiwa, Y. / Ueda, T. / Imoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kxx.cif.gz | 33.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kxx.ent.gz | 25.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kxx_validation.pdf.gz | 405.7 KB | Display | wwPDB validaton report |
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Full document | 1kxx_full_validation.pdf.gz | 406.8 KB | Display | |
Data in XML | 1kxx_validation.xml.gz | 7.4 KB | Display | |
Data in CIF | 1kxx_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/1kxx ftp://data.pdbj.org/pub/pdb/validation_reports/kx/1kxx | HTTPS FTP |
-Related structure data
Related structure data | 1kxwC 1kxyC 1rfpSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Mutation: D18N, N27D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: HEN LYSOZYME / Gene (production host): HEN LYSOZYME / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SACCHAROMYCES CEREVISIAE / References: UniProt: P00698, lysozyme |
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#2: 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: 2.08 Å3/Da / Density % sol: 40.78 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 / Details: 50 MM ACETATE AT PH 4.7 CONTAINING 0.9 M NACL | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 5.5 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 5, 1996 |
Radiation | Monochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→100 Å / Num. obs: 11446 / % possible obs: 83.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.0682 |
Reflection shell | Resolution: 1.71→1.8 Å / Rmerge(I) obs: 0.32 / % possible all: 51.3 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 1RFP Resolution: 1.71→6 Å / Data cutoff low absF: 1 / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 1.71→6 Å
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refine LS restraints | *PLUS
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