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Open data
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Basic information
Entry | Database: PDB / ID: 1lj3 | ||||||
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Title | CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN AT PH 4.6 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Hydration of Proteins | ||||||
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 | ![]() | ||||||
![]() | Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M. | ||||||
![]() | ![]() Title: Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme. Authors: Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M. #1: ![]() Title: The Effect of Stabilizing Additives on the Structure and Hydration of Proteins: A Study Involving Tetragonal Lysozyme Authors: Datta, S. / Biswal, B.K. / Vijayan, M. #2: ![]() Title: An X-Ray Analysis of Native Monoclinic Lysozyme. A Case Study on the Reliability of Refined Protein Structures and a Comparison with the Low-Humidity Form in Relation to Mobility and Enzyme Action Authors: Nagendra, H.G. / Sudarsanakumar, C. / Vijayan, 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 | ![]() | 63.7 KB | Display | ![]() |
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PDB format | ![]() | 50.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lj4C ![]() 1ljeC ![]() 1ljfC ![]() 1ljgC ![]() 1ljhC ![]() 1ljiC ![]() 1ljjC ![]() 1ljkC 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.15 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 4.6 Details: Sodium Acetate (0.1M) Buffer, Sodium Nitrate (0.44M) Precipitant, pH 4.6, LIQUID DIFFUSION at 298K |
Crystal grow | *PLUS Temperature: 293 K / Method: unknown |
Components of the solutions | *PLUS Conc.: 0.1 M / Common name: sodium acetate / Details: pH4.6 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 13344 / Biso Wilson estimate: 21.9 Å2 |
Reflection shell | Resolution: 2→2.07 Å |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 13653 / % possible obs: 96.7 % / Num. measured all: 39179 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 95.7 % / Num. unique obs: 1311 / Rmerge(I) obs: 0.161 |
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Processing
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Refinement | Resolution: 2→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 362599.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.436 Å2 / ksol: 0.336598 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 30 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3 |