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Open data
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Basic information
Entry | Database: PDB / ID: 1lz8 | ||||||
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Title | LYSOZYME PHASED ON ANOMALOUS SIGNAL OF SULFURS AND CHLORINES | ||||||
![]() | PROTEIN (LYSOZYME) | ||||||
![]() | HYDROLASE / O-GLYCOSYL / GLYCOSIDASE | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dauter, Z. / Dauter, M. / De La Fortelle, E. / Bricogne, G. / Sheldrick, G.M. | ||||||
![]() | ![]() Title: Can anomalous signal of sulfur become a tool for solving protein crystal structures? Authors: Dauter, Z. / Dauter, M. / de La Fortelle, E. / Bricogne, G. / Sheldrick, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 44.4 KB | Display | ![]() |
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PDB format | ![]() | 30.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8lyzS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: 8 CHLORIDE AND 1 SODIUM ION PRESENT / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40 % | ||||||||||||||||||
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Crystal grow | pH: 4.6 Details: BATCH METHOD. 20 MG/ML PROTEIN SOLUTION IN 50MM SODIUM ACETATE PH 4.6 AND 10% NACL. CRYSTALS GROWN AT ROOM TEMPERATURE. | ||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||
Crystal grow | *PLUS Method: batch method | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1994 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.927 Å / Relative weight: 1 |
Reflection | Resolution: 0.92→25 Å / Num. obs: 58373 / % possible obs: 90.1 % / Observed criterion σ(I): 3 / Redundancy: 2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 29.1 |
Reflection shell | Resolution: 0.93→0.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 4.9 / Rsym value: 0.17 / % possible all: 78 |
Reflection | *PLUS Highest resolution: 1.53 Å / Lowest resolution: 60 Å / % possible obs: 100 % / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS Highest resolution: 1.53 Å / Lowest resolution: 1.56 Å / % possible obs: 100 % / Rmerge(I) obs: 0.19 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 8LYZ Resolution: 1.53→25 Å / SU B: 1.753 / SU ML: 0.067 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.128
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Displacement parameters | Biso mean: 19.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→25 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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