+Open data
-Basic information
Entry | Database: PDB / ID: 1ckd | ||||||
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Title | T43V MUTANT HUMAN LYSOZYME | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE / STABILITY / HYDROGEN BOND | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / OTHER / Resolution: 1.8 Å | ||||||
Authors | Takano, K. / Yamagata, Y. / Funahashi, J. / Yutani, K. | ||||||
Citation | 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 | 1ckd.cif.gz | 43.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ckd.ent.gz | 29.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ckd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/1ckd ftp://data.pdbj.org/pub/pdb/validation_reports/ck/1ckd | HTTPS FTP |
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-Related structure data
Related structure data | 1cj6C 1cj7C 1cj8C 1cj9C 1ckcC 1ckfC 1ckgC 1ckhC 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: 14718.719 Da / Num. of mol.: 1 / Mutation: T43V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: SYNTHETIC GENE / 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: 1.99 Å3/Da / Density % sol: 38.22 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: protein solution is mixed in a 1:1 ratio with well solution | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 1, 1997 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 11166 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.044 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 10.7 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 32373 |
Reflection shell | *PLUS % possible obs: 95.9 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: WILD-TYPE OF HUMAN LYSOZYME Resolution: 1.8→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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