+Open data
-Basic information
Entry | Database: PDB / ID: 4dt3 | ||||||
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Title | Crystal structure of zinc-charged lysozyme | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme | ||||||
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 / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||
Authors | An, Y.J. / Jeong, C.S. / Cha, S.S. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Experimental phasing using zinc anomalous scattering Authors: Cha, S.S. / An, Y.J. / Jeong, C.S. / Kim, M.K. / Lee, S.G. / Lee, K.H. / Oh, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dt3.cif.gz | 36.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dt3.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dt3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/4dt3 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/4dt3 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ, LYZ1 / Plasmid: pBR322 / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.01 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 295 K / Method: microbath / pH: 4 Details: 0.1M citric acid, 1M NaCl, pH 4.0, microbath, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.28286 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 19, 2010 |
Radiation | Monochromator: Zn wavelength / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.28286 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 11466 / % possible obs: 99.9 % / Biso Wilson estimate: 13 Å2 |
Reflection shell | Resolution: 1.79→1.85 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→33.38 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 184727.25 / 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: 52.4614 Å2 / ksol: 0.371961 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 14.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→33.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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