+Open data
-Basic information
Entry | Database: PDB / ID: 8s2u | |||||||||
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Title | SSX structure of Lysozyme grown in batch conditions | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Stubbs, J. / Tews, I. / Maly, M. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Iucrj / Year: 2024 Title: Droplet microfluidics for time-resolved serial crystallography. Authors: Stubbs, J. / Hornsey, T. / Hanrahan, N. / Esteban, L.B. / Bolton, R. / Maly, M. / Basu, S. / Orlans, J. / de Sanctis, D. / Shim, J.U. / Shaw Stewart, P.D. / Orville, A.M. / Tews, I. / West, J. #1: Journal: BioRxiv / Year: 2024 Title: Droplet microfluidics for time-resolved serial crystallography Authors: Stubbs, J. / Tews, I. / Maly, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8s2u.cif.gz | 44 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8s2u.ent.gz | 27.5 KB | Display | PDB format |
PDBx/mmJSON format | 8s2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8s2u_validation.pdf.gz | 400.8 KB | Display | wwPDB validaton report |
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Full document | 8s2u_full_validation.pdf.gz | 400.8 KB | Display | |
Data in XML | 8s2u_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 8s2u_validation.cif.gz | 9.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/8s2u ftp://data.pdbj.org/pub/pdb/validation_reports/s2/8s2u | HTTPS FTP |
-Related structure data
Related structure data | 8s2vC 8s2wC 8s2xC 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: 16257.660 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 | #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: 2.06 Å3/Da / Density % sol: 40.38 % |
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Crystal grow | Temperature: 294 K / Method: batch mode / pH: 3 Details: Protein dissolved in 20 mM sodium acetate pH 4.6 Protein and precipitant mixed in a 1:4 ratio Precipitant solution: 6% PEG 6000 (w/v), 3.4M NaCl and 1M sodium acetate pH 3.0 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07 Å |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Jan 23, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→79 Å / Num. obs: 11636 / % possible obs: 100 % / Redundancy: 438 % / Biso Wilson estimate: 30.46 Å2 / CC1/2: 0.99 / CC star: 0.99 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 47.67 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 669 / CC1/2: 0.49 / CC star: 0.81 / % possible all: 100 |
Serial crystallography sample delivery | Description: SOS Chip / Method: fixed target |
Serial crystallography data reduction | Crystal hits: 34032 / Frames indexed: 29954 / Frames total: 81800 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→55.924 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.148 / SU B: 3.927 / SU ML: 0.108 / Average fsc free: 0.9331 / Average fsc work: 0.9534 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.133 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.199 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→55.924 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: 20
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