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Yorodumi- PDB-2zq4: The crystal structure of the orthorhombic form of hen egg white l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zq4 | ||||||
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Title | The crystal structure of the orthorhombic form of hen egg white lysozyme at 2.0 angstroms resolution | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / lysozyme / HEWL / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / Hirose, M. | ||||||
Citation | Journal: To be Published Title: The crystal structure of the orthorhombic form of hen egg white lysozyme at 1.5 angstroms resolution Authors: Aibara, S. / Suzuki, A. / Kidera, A. / Shibata, K. / Yamane, T. / DeLucas, L.J. / Hirose, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zq4.cif.gz | 34.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zq4.ent.gz | 26.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/2zq4 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/2zq4 | HTTPS FTP |
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-Related 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 / Source: (natural) Gallus gallus (chicken) / 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: 2.22 Å3/Da / Density % sol: 44.58 % |
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Crystal grow | Temperature: 310 K / Details: 310K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS VII / 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→10 Å / Num. obs: 8115 / % possible obs: 87.9 % / Biso Wilson estimate: 3 Å2 / Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→9.87 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 7948193.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 57.3301 Å2 / ksol: 0.397336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→9.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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