+Open data
-Basic information
Entry | Database: PDB / ID: 7s2g | ||||||
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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 / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Lima, L.M.T.R. / Ramos, N.G. / Ribeiro, F.S. | ||||||
Funding support | Brazil, 1items
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Citation | Journal: Anal.Biochem. / Year: 2022 Title: The reproducible normality of the crystallographic B-factor. Authors: Ramos, N.G. / Sarmanho, G.F. / de Sa Ribeiro, F. / de Souza, V. / Lima, L.M.T.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s2g.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s2g.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 7s2g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s2g_validation.pdf.gz | 421.1 KB | Display | wwPDB validaton report |
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Full document | 7s2g_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 7s2g_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 7s2g_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/7s2g ftp://data.pdbj.org/pub/pdb/validation_reports/s2/7s2g | HTTPS FTP |
-Related structure data
Related structure data | 7s27C 7s28C 7s29C 7s2aC 7s2bC 7s2cC 7s2dC 7s2eC 7s2fC 7s2qC 7s2uC 7s2vC 7s2wC 7s30C 7s31C 7s32C 7s33C 7s34C 7s35C 6qwyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: egg white / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-NA / |
#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: 1.97 Å3/Da / Density % sol: 37.49 % |
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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 | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS 3.0 MICROFOCUS / Wavelength: 1.54184 Å | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Dec 12, 2020 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.595→25.42 Å / Num. obs: 29913 / % possible obs: 99.67 % / Redundancy: 9.73 % / Rsym value: 0.158 / Net I/av σ(I): 228.999 / Net I/σ(I): 6.44 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6qwy Resolution: 1.6→25.42 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2473 / WRfactor Rwork: 0.207 / FOM work R set: 0.8489 / SU B: 2.252 / SU ML: 0.08 / SU R Cruickshank DPI: 0.1136 / SU Rfree: 0.1142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.114 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: isomorphous replacement with REFMAC , restrained refinement with REFMAC, real space refinement with C.O.O.T.
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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 max: 46.16 Å2 / Biso mean: 13.436 Å2 / Biso min: 2.08 Å2
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Refinement step | Cycle: final / Resolution: 1.6→25.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.637 Å / Rfactor Rfree error: 0
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