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Yorodumi- PDB-1c7p: CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME WITH FOUR EXTRA RESIDU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c7p | ||||||
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Title | CRYSTAL STRUCTURE OF MUTANT HUMAN LYSOZYME WITH FOUR EXTRA RESIDUES (EAEA) AT THE N-TERMINAL | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / EXTRA N-TERMINAL RESIDUES | ||||||
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 / Resolution: 2.4 Å | ||||||
Authors | Goda, S. / Takano, K. / Yamagata, Y. / Katakura, Y. / Yutani, K. | ||||||
Citation | Journal: Protein Eng. / Year: 2000 Title: Effect of extra N-terminal residues on the stability and folding of human lysozyme expressed in Pichia pastoris. Authors: Goda, S. / Takano, K. / Yamagata, Y. / Katakura, Y. / Yutani, K. #1: Journal: Eur.J.Biochem. / Year: 1999 Title: Effect of Foreign N-terminal Residues on the Conformational Stability of Human Lysozyme Authors: Takano, K. / Tsuchimori, K. / Yamagata, Y. / Yutani, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c7p.cif.gz | 42.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c7p.ent.gz | 29.7 KB | Display | PDB format |
PDBx/mmJSON format | 1c7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c7p ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c7p | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 15121.078 Da / Num. of mol.: 1 / Mutation: T15E, V16A, Q17E, G18A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / References: UniProt: P61626, lysozyme | ||
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#2: Chemical | #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: 3.67 Å3/Da / Density % sol: 66.49 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: cadmium chloride, sodium acetate, PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃Details: equal volume of protein and reservoir solution were used for the drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 15, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.4 Å / Num. all: 72761 / Num. obs: 9367 / % possible obs: 99.9 % / Rmerge(I) obs: 0.044 |
Reflection | *PLUS Num. measured all: 72761 |
-Processing
Software |
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Refinement | Resolution: 2.4→5 Å /
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Refinement step | Cycle: LAST / Resolution: 2.4→5 Å
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Refine LS restraints |
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