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- PDB-6f9x: Lysozyme crystallized in presence of 100 mM lithium sulphate at pH 4.5 -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f9x | ||||||
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Title | Lysozyme crystallized in presence of 100 mM lithium sulphate at pH 4.5 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Camara-Artigas, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Orthorhombic lysozyme crystallization at acidic pH values driven by phosphate binding. Authors: Plaza-Garrido, M. / Salinas-Garcia, M.C. / Camara-Artigas, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88 KB | Display | ![]() |
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PDB format | ![]() | 65.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.1 KB | Display | ![]() |
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Full document | ![]() | 421.1 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6f1lC ![]() 6f1mC ![]() 6f1oC ![]() 6f1pC ![]() 6f1rC ![]() 6f9yC ![]() 6f9zC ![]() 6fa0C ![]() 4e3uS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14060.808 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.08 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100 mM Lithium Sulphate, 0.3 M Sodium Chloride, 0.1 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: CHANNEL-CUT MONOCHROMATOR AND A KIRKPATRICK-BAEZ (KB) FOCUSING SYSTEM Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→19.77 Å / Num. obs: 30557 / % possible obs: 86.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 13.36 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.028 / Rrim(I) all: 0.064 / Net I/σ(I): 12.8 / Num. measured all: 155400 / Scaling rejects: 42 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4E3U Resolution: 1.25→19.775 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0.1 / Phase error: 20.34 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.69 Å2 / Biso mean: 18.0392 Å2 / Biso min: 8.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.25→19.775 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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