+Open data
-Basic information
Entry | Database: PDB / ID: 1b7s | ||||||
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Title | VERIFICATION OF SPMP USING MUTANT HUMAN LYSOZYMES | ||||||
Components | LYSOZYME | ||||||
Keywords | MUTANT STABILITY / HUMAN LYSOZYME | ||||||
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 / SYNCHROTRON / ISOMORPHOUS METHOD / Resolution: 2 Å | ||||||
Authors | Takano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K. | ||||||
Citation | Journal: Protein Eng. / Year: 1999 Title: Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes. Authors: Takano, K. / Ota, M. / Ogasahara, K. / Yamagata, Y. / Nishikawa, K. / Yutani, K. #1: Journal: J.Mol.Biol. / Year: 1998 Title: A General Rule for the Relationship between Hydrophobic Effect and Conformational Stability of a Protein: Stability and Structure of a Series of Hydrophobic Mutants of Human Lysozyme Authors: Takano, K. / Yamagata, Y. / Yutani, K. #2: Journal: Biochemistry / Year: 1998 Title: Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine--> Phenylalanine Mutants Authors: Yamagata, Y. / Kubota, M. / Sumikawa, Y. / Funahashi, J. / Takano, K. / Fujii, S. / Yutani, K. #3: Journal: Biochemistry / Year: 1997 Title: Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants Authors: Takano, K. / Yamagata, Y. / Fujii, S. / Yutani, K. #4: Journal: J.Mol.Biol. / Year: 1997 Title: Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability Authors: Takano, K. / Funahashi, J. / Yamagata, Y. / Fujii, S. / Yutani, K. #5: Journal: J.Mol.Biol. / Year: 1995 Title: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants Authors: Takano, K. / Ogasahara, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b7s.cif.gz | 39.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b7s.ent.gz | 30.4 KB | Display | PDB format |
PDBx/mmJSON format | 1b7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b7s ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b7s | HTTPS FTP |
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-Related structure data
Related structure data | 1b7lC 1b7mC 1b7nC 1b7oC 1b7pC 1b7qC 1b7rC 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: 14708.639 Da / Num. of mol.: 1 / Mutation: V74S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P61626 |
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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: 1.91 Å3/Da / Density % sol: 35.45 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.5 / Details: pH 4.5 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / 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: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 |
Detector | Detector: IMAGE PLATE / Date: Apr 10, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 21097 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rmerge(I) obs: 0.056 |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 81.2 |
Reflection | *PLUS Num. obs: 7151 / Num. measured all: 21097 |
-Processing
Software |
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Refinement | Method to determine structure: ISOMORPHOUS METHOD Starting model: WILD-TYPE OF HUMAN LYSOZYME Resolution: 2→8 Å / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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