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Yorodumi- PDB-1jiy: CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE 20% SO... -
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-Basic information
Entry | Database: PDB / ID: 1jiy | ||||||
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Title | CRYSTAL STRUCTURE OF TETRAGONAL LYSOZYME GROWN IN PRESENCE 20% SORBITOL | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / ENZYME-TETRAGONAL FORM / MUCOPEPTIDE N-ACETYLMURAMYL HYDROLASE / HEN EGG-WHITE LYSOZYME | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Datta, S. / Biswal, B.K. / Vijayan, M. | ||||||
Citation | 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. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Hydration, Mobility and Accessibility of Lysozyme: Strucutres of a Ph 6.5 Orthorhombic Form and its Low-Humidity Variant and a Comparative Study Involving 20 Crystallographically Independent Molecules Authors: Biswal, B.K. / Sukumar, N. / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1993 Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content Authors: Madhusudan, K. / Kodandapani, R. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jiy.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jiy.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jiy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jiy_validation.pdf.gz | 422.6 KB | Display | wwPDB validaton report |
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Full document | 1jiy_full_validation.pdf.gz | 424.2 KB | Display | |
Data in XML | 1jiy_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 1jiy_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1jiy ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1jiy | HTTPS FTP |
-Related structure data
Related structure data | 1jisC 1jitC 1jj0C 1jj1C 1jj3C 193lS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOPLASM / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme |
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#2: 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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.6 Details: Na-acetate buffer, pH 4.6, 10% NaCl, 20% sorbitol, LIQUID DIFFUSION at 293K |
Crystal grow | *PLUS Method: unknown |
Components of the solutions | *PLUS Conc.: 0.04 M / Common name: acetate / Details: pH4.6 |
-Data collection
Diffraction | Mean temperature: 293 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: 1.85→30 Å / Num. all: 10830 / Num. obs: 10776 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.086 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.85→1.92 Å / Num. unique all: 1043 / Rsym value: 0.328 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 120501 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 100 % / Num. unique obs: 10043 / Rmerge(I) obs: 0.328 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 514255.43 / 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: 45.8735 Å2 / ksol: 0.368105 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.19 / Rfactor Rfree: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.238 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.198 |