+Open data
-Basic information
Entry | Database: PDB / ID: 8k8m | ||||||
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Title | Crystallographic structure of Lysozyme C from chicken | ||||||
Components | Lysozyme C | ||||||
Keywords | ANTIMICROBIAL PROTEIN / chicken egg | ||||||
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: 1.6 Å | ||||||
Authors | Zheng, P. / Shang, G. / Jin, J. / He, L. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Crystallographic structure of Lysozyme C from chicken Authors: Zheng, P. / Shang, G. / Jin, J. / He, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k8m.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k8m.ent.gz | 28.5 KB | Display | PDB format |
PDBx/mmJSON format | 8k8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k8m_validation.pdf.gz | 440.5 KB | Display | wwPDB validaton report |
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Full document | 8k8m_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 8k8m_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 8k8m_validation.cif.gz | 13.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/8k8m ftp://data.pdbj.org/pub/pdb/validation_reports/k8/8k8m | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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 / Source: (natural) Gallus gallus (chicken) / Cell line: egg / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.3 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 4.6 / Details: 5%(w/v) NaCl, 0.1M Na acetate pH4.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54056 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jul 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→55 Å / Num. obs: 16043 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.022 / Rrim(I) all: 0.066 / Χ2: 0.97 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.583 / Num. measured all: 4510 / Num. unique obs: 784 / CC1/2: 0.808 / Rpim(I) all: 0.265 / Rrim(I) all: 0.642 / Χ2: 1.11 / Net I/σ(I) obs: 3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→55 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.591 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.088 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→55 Å
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