+Open data
-Basic information
Entry | Database: PDB / ID: 7s33 | ||||||
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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. | ||||||
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 | 7s33.cif.gz | 42.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s33.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 7s33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s33_validation.pdf.gz | 417.7 KB | Display | wwPDB validaton report |
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Full document | 7s33_full_validation.pdf.gz | 417.8 KB | Display | |
Data in XML | 7s33_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 7s33_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s3/7s33 ftp://data.pdbj.org/pub/pdb/validation_reports/s3/7s33 | HTTPS FTP |
-Related structure data
Related structure data | 7s27C 7s28C 7s29C 7s2aC 7s2bC 7s2cC 7s2dC 7s2eC 7s2fC 7s2gC 7s2qC 7s2uC 7s2vC 7s2wC 7s30C 7s31C 7s32C 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: 2.01 Å3/Da / Density % sol: 38.78 % / Mosaicity: 0.93 ° |
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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: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.54056 Å | ||||||||||||||||||||||||
Detector | Type: OXFORD TITAN CCD / Detector: CCD / Date: Dec 12, 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→13.62 Å / Num. obs: 15719 / % possible obs: 98.5 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.1 / Num. measured all: 72511 / Scaling rejects: 259 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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→13.62 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1876 / WRfactor Rwork: 0.1766 / FOM work R set: 0.8591 / SU B: 1.741 / SU ML: 0.059 / SU R Cruickshank DPI: 0.0967 / SU Rfree: 0.0876 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.088 / 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: 58.58 Å2 / Biso mean: 14.809 Å2 / Biso min: 2.17 Å2
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Refinement step | Cycle: final / Resolution: 1.6→13.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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