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Yorodumi- PDB-1lji: CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE 10% SO... -
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-Basic information
Entry | Database: PDB / ID: 1lji | ||||||
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Title | CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE 10% SORBITOL | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Hydration of Proteins | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2002 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: Journal: Acta Crystallogr.,Sect.D / Year: 2001 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: Journal: Acta Crystallogr.,Sect.D / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lji.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lji.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 1lji.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lji_validation.pdf.gz | 449.1 KB | Display | wwPDB validaton report |
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Full document | 1lji_full_validation.pdf.gz | 453.1 KB | Display | |
Data in XML | 1lji_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 1lji_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/1lji ftp://data.pdbj.org/pub/pdb/validation_reports/lj/1lji | HTTPS FTP |
-Related structure data
Related structure data | 1lj3C 1lj4C 1ljeC 1ljfC 1ljgC 1ljhC 1ljjC 1ljkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.86 % | ||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.6 Details: Sodium Acetate (0.1M) Buffer, Sodium Nitrate (0.44M) Precipitant, pH 4.6, LIQUID DIFFUSION at 293K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
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: 13423 / Biso Wilson estimate: 20 Å2 |
Reflection | *PLUS Highest resolution: 2 Å / Num. obs: 13571 / % possible obs: 96.4 % / Num. measured all: 61435 / Rmerge(I) obs: 0.075 |
Reflection shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / % possible obs: 94.2 % / Num. unique obs: 1290 / Rmerge(I) obs: 0.165 |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 452694.9 / 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: 47.9242 Å2 / ksol: 0.356822 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 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: 0.02 / 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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