+Open data
-Basic information
Entry | Database: PDB / ID: 1bgi | ||||||
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Title | ORTHORHOMBIC LYSOZYME CRYSTALLIZED AT HIGH TEMPERATURE (310K) | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / O-GLYCOSYL | ||||||
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: 1.7 Å | ||||||
Authors | Oki, H. / Matsuura, Y. / Komatsu, H. / Chernov, A.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: Refined structure of orthorhombic lysozyme crystallized at high temperature: correlation between morphology and intermolecular contacts. Authors: Oki, H. / Matsuura, Y. / Komatsu, H. / Chernov, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bgi.cif.gz | 34.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bgi.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1bgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/1bgi ftp://data.pdbj.org/pub/pdb/validation_reports/bg/1bgi | HTTPS FTP |
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-Related structure data
Related structure data | 2lztS 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: ORTHORHOMBIC CRYSTAL FORM / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.2 Å3/Da / Density % sol: 44 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 310 K / Method: batch method / pH: 4.7 Details: CRYSTALLIZATION WAS PERFORMED BY THE BATCH METHOD AT 310 K. THE SAME WAY AS DESCRIBED BY JOLLES AND BERTHOU (1972)., pH 4.7, batch method | ||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 310 K / Method: batch method | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Jul 6, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→12 Å / Num. obs: 11992 / % possible obs: 82.6 % / Observed criterion σ(I): 1 / Redundancy: 1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LZT Resolution: 1.7→12 Å / σ(F): 1 /
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Displacement parameters | Biso mean: 19.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→12 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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