+Open data
-Basic information
Entry | Database: PDB / ID: 8fpr | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hen egg white lysozyme | ||||||
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: 1.6 Å | ||||||
Authors | Lima, L.M.T.R. / Ramos, N.G. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: To Be Published Title: Crystal structure of hen egg white lysozyme Authors: Lima, L.M.T.R. / Ramos, N.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8fpr.cif.gz | 43.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8fpr.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 8fpr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fpr_validation.pdf.gz | 831.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8fpr_full_validation.pdf.gz | 832.1 KB | Display | |
Data in XML | 8fpr_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 8fpr_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/8fpr ftp://data.pdbj.org/pub/pdb/validation_reports/fp/8fpr | HTTPS FTP |
-Related structure data
Related structure data | 8fp6C 8fp7C 8fp8C 8fpbC 8fpdC 8fpmC 8fpnC 8fppC 8fpuC 8fryC 8fs0C 8fs9C 8fsaC 8fscC 8fsfC 8fsgC 8fshC 8fsmC 8fsnC 8fstC 8fsuC 8fsvC 8fswC 8fsxC 8fsyC 8ft0C 8ft1C 8ft2C 8ft3C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: lyzozyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
---|---|
#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
---|---|
Crystal grow | Temperature: 295 K / Method: evaporation / pH: 4.6 Details: 1.2 M NaCl, 100 mM Sodium Acetate, 50 mg/mL Lyzozyme, 30% Glycerol for cryoprotection |
-Data collection
Diffraction | Mean temperature: 125 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å |
Detector | Type: OXFORD TITAN CCD / Detector: CCD / Date: Sep 4, 2020 |
Radiation | Monochromator: Ni Filter / 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→13.43 Å / Num. obs: 15432 / % possible obs: 99.5 % / Redundancy: 4.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.049 / Rrim(I) all: 0.118 / Χ2: 0.72 / Net I/σ(I): 6.9 / Num. measured all: 72102 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 99.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.974 / Num. measured all: 2272 / Num. unique obs: 778 / CC1/2: 0.589 / Rpim(I) all: 0.68 / Rrim(I) all: 1.194 / Χ2: 0.4 / Net I/σ(I) obs: 0.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→13.43 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.3 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.6→13.43 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|