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Yorodumi- PDB-1di5: ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABIL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1di5 | ||||||
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Title | ROLE OF AMINO ACID RESIDUES AT TURNS IN THE CONFORMATIONAL STABILITY AND FOLDING OF HUMAN LYSOZYME | ||||||
Components | LYSOZYME C | ||||||
Keywords | HYDROLASE / STABILITY / TURN / MUTANT | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å | ||||||
Authors | Takano, K. / Yamagata, Y. / Yutani, K. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Role of amino acid residues at turns in the conformational stability and folding of human lysozyme. Authors: Takano, K. / Yamagata, Y. / Yutani, K. #1: Journal: Biochemistry / Year: 1999 Title: Contribution of Intra-and Intermolecular Hydrogen Bonds to the Conformational Stability of Human Lysozyme Authors: Takano, K. / Yamagata, Y. / Funahashi, J. / Hioki, Y. / Kuramitsu, S. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1di5.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1di5.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 1di5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1di5_validation.pdf.gz | 368.4 KB | Display | wwPDB validaton report |
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Full document | 1di5_full_validation.pdf.gz | 368.2 KB | Display | |
Data in XML | 1di5_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1di5_validation.cif.gz | 6.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/1di5 ftp://data.pdbj.org/pub/pdb/validation_reports/di/1di5 | 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: Protein | Mass: 14563.500 Da / Num. of mol.: 1 / Mutation: DEL 101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEL125 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61626, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: 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: 1.96 Å3/Da / Density % sol: 37.34 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: SODIUM PHOSPHATE, SODIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Details: Takano, K., (1995) J.Mol.Biol., 254, 62. | ||||||||||||||||||||||||
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 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 25, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 27719 / Num. obs: 5952 / % possible obs: 97.3 % / Rmerge(I) obs: 0.042 |
Reflection shell | Resolution: 2.2→2.24 Å / Rmerge(I) obs: 0.088 / % possible all: 84.3 |
Reflection | *PLUS Num. measured all: 27719 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 8 Å / σ(F): 3 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS |