+Open data
-Basic information
Entry | Database: PDB / ID: 4d9z | ||||||
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Title | Lysozyme at 318K | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE | ||||||
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: 1.709 Å | ||||||
Authors | Sharma, P. / Ashish | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Characterization of heat induced spherulites of lysozyme reveals new insight on amyloid initiation Authors: Sharma, P. / Verma, N. / Singh, P.K. / Korpole, S. / Ashish | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4d9z.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4d9z.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 4d9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4d9z_validation.pdf.gz | 432.8 KB | Display | wwPDB validaton report |
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Full document | 4d9z_full_validation.pdf.gz | 432.9 KB | Display | |
Data in XML | 4d9z_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 4d9z_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/4d9z ftp://data.pdbj.org/pub/pdb/validation_reports/d9/4d9z | HTTPS FTP |
-Related structure data
Related structure data | 4dc4C 4eofC 4ii8C 4r0fC 1bgiS 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
#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: Chemical | ChemComp-CL / #3: Chemical | ChemComp-GOL / | #4: Chemical | #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: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 318 K / Method: vapor diffusion, hanging drop / pH: 3.8 Details: 50mM sodium acetate, 1-1.5M NaCl, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 318K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2011 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.709→50 Å / Num. all: 13859 / Num. obs: 13859 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 18.24 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 32.35 |
Reflection shell | Resolution: 1.71→1.74 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.061 / Mean I/σ(I) obs: 20.9 / Num. unique all: 667 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BGI Resolution: 1.709→21.363 Å / SU ML: 0.37 / Isotropic thermal model: Isotropic / σ(F): 1.44 / Phase error: 17.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.04 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.709→21.363 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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