+Open data
-Basic information
Entry | Database: PDB / ID: 2z2f | ||||||
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Title | X-ray Crystal Structure of Bovine Stomach Lysozyme | ||||||
Components | Lysozyme C-2 | ||||||
Keywords | HYDROLASE / LYSOZYME C / Stomach Lysozyme / 1 / 4-BETA-N-Acetylmuramidase C / Bacteriolytic enzyme | ||||||
Function / homology | Function and homology information cytolysis / metabolic process / digestion / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Akieda, D. / Nonaka, Y. / Watanabe, N. / Tanaka, I. / Kamiya, M. / Aizawa, T. / Nitta, K. / Demura, M. / Kawano, K. | ||||||
Citation | Journal: To be Published Title: Stability of Bovine Stomach Lysozyme in Acidic Condition Authors: Akieda, D. / Nonaka, Y. / Watanabe, N. / Tanaka, I. / Kamiya, M. / Aizawa, T. / Nitta, K. / Demura, M. / Kawano, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2z2f.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z2f.ent.gz | 30.5 KB | Display | PDB format |
PDBx/mmJSON format | 2z2f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z2/2z2f ftp://data.pdbj.org/pub/pdb/validation_reports/z2/2z2f | HTTPS FTP |
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-Related structure data
Related structure data | 1lz1S 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: 14433.230 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pPIC3 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: Q06283, lysozyme | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: 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: 1.94 Å3/Da / Density % sol: 36.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 18772 / Num. obs: 17833 / % possible obs: 95 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.074 Å2 / Net I/σ(I): 36.374 |
Reflection shell | Resolution: 1.5→1.55 Å / Mean I/σ(I) obs: 17.272 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LZ1 Resolution: 1.5→17.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.041 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.088 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→17.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.498→1.537 Å / Total num. of bins used: 20
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