+Open data
-Basic information
Entry | Database: PDB / ID: 1jse | ||||||
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Title | FULL-MATRIX LEAST-SQUARES REFINEMENT OF TURKEY LYSOZYME | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL / TURKEY LYSOZYME / ENZYME | ||||||
Function / homology | Function and homology information glycosaminoglycan binding / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Meleagris gallopavo (turkey) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Harata, K. / Abe, Y. / Muraki, M. | ||||||
Citation | Journal: Proteins / Year: 1998 Title: Full-matrix least-squares refinement of lysozymes and analysis of anisotropic thermal motion. Authors: Harata, K. / Abe, Y. / Muraki, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jse.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jse.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 1jse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/js/1jse ftp://data.pdbj.org/pub/pdb/validation_reports/js/1jse | HTTPS FTP |
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-Related structure data
Related structure data | 1jsfC 1lz3 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: 14228.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00703, lysozyme |
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#2: Chemical | ChemComp-POL / |
#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: 35.6 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.2 Details: 2.2M AMMONIUM SULFATE SOLUTION AT PH 4.2 CONTAINING 10% 1-PROPANOL AND 4% PROTEIN | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: AREA DETECTOR / Date: Jan 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→22.3 Å / Num. obs: 36320 / % possible obs: 86.1 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.12→1.14 Å / Rmerge(I) obs: 0.227 / % possible all: 53.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ3 1lz3 Resolution: 1.12→22.3 Å / Num. parameters: 10631 / Num. restraintsaints: 12784 / Cross valid method: FREE R / σ(F): 0
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Solvent computation | Solvent model: SWAT | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→22.3 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.14 / Rfactor Rwork: 0.103 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |