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Yorodumi- PDB-1lz9: ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lz9 | ||||||
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Title | ANOMALOUS SIGNAL OF SOLVENT BROMINES USED FOR PHASING OF LYSOZYME | ||||||
Components | PROTEIN (LYSOZYME) | ||||||
Keywords | HYDROLASE / LYSOZYME / SOLVENT BROMIDES / ANOMALOUS DISPERSION / SINGLE WAVELENGTH | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / 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 / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Dauter, Z. / Dauter, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Anomalous signal of solvent bromides used for phasing of lysozyme. Authors: Dauter, Z. / Dauter, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lz9.cif.gz | 44.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lz9.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 1lz9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/1lz9 ftp://data.pdbj.org/pub/pdb/validation_reports/lz/1lz9 | 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 |
-Links
-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: BROMIDE AND SODIUM IONS PRESENT / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | ChemComp-BR / #3: Chemical | ChemComp-NA / | #4: 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: 2.05 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.6 Details: CRYSTALLIZED IN HANGING DROPS. 15 MG/ML PROTEIN SOLUTION IN 100 MM SODIUM ACETATE PH 4.6 AND 1 M SODIUM BROMIDE. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: NSLS / Beamline: X9B / Wavelength: 0.9188, 0.9195, 0.9198, 0.9201 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: BENT MIRROR | |||||||||||||||
Radiation | Monochromator: SILICON CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→20 Å / Num. obs: 13429 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.035 / Rsym value: 0.035 / Net I/σ(I): 50.2 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 10 / Rsym value: 0.182 / % possible all: 80 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 8LYZ Resolution: 1.7→20 Å / SU B: 2.7 / SU ML: 0.094 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.162
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Displacement parameters | Biso mean: 17.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |