+Open data
-Basic information
Entry | Database: PDB / ID: 3n9a | ||||||
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Title | Mite-y Lysozyme: Vegemite | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / 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 / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / 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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Newman, J. / Peat, T.S. / Lucent, D. | ||||||
Citation | Journal: To be Published Title: Mite-y Lysozyme Crystals and Structures Authors: Newman, J. / Peat, T.S. / Lucent, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3n9a.cif.gz | 42.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n9a.ent.gz | 29.3 KB | Display | PDB format |
PDBx/mmJSON format | 3n9a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/3n9a ftp://data.pdbj.org/pub/pdb/validation_reports/n9/3n9a | HTTPS FTP |
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-Related structure data
Related structure data | 3n9cC 3n9eC 2blxS 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 / Details: Purchased from Sigma / Source: (natural) Gallus gallus (chicken) / 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: 2.08 Å3/Da / Density % sol: 40.8 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.5 Details: Crystals were obtained by counter diffusion in capillary tubes stuck into Vegemite., pH 4.5, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→39.7 Å / Num. obs: 23901 / % possible obs: 98 % / Redundancy: 18.6 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 6.1 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BLX Resolution: 1.4→31.39 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.925 / SU ML: 0.037 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.063 / 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: 19.385 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→31.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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