+Open data
-Basic information
Entry | Database: PDB / ID: 8ezp | |||||||||
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Title | Lysozyme Anomalous Dataset at 260 K and 7.1 keV | |||||||||
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 / SAD / Resolution: 1.9 Å | |||||||||
Authors | Doukov, T. / Yabukarski, F. / Herschlag, D. | |||||||||
Funding support | United States, France, 2items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures. Authors: Doukov, T. / Herschlag, D. / Yabukarski, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ezp.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ezp.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 8ezp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ezp_validation.pdf.gz | 434 KB | Display | wwPDB validaton report |
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Full document | 8ezp_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 8ezp_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 8ezp_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/8ezp ftp://data.pdbj.org/pub/pdb/validation_reports/ez/8ezp | HTTPS FTP |
-Related structure data
Related structure data | 8ezoC 8ezuC 8ezxC 8f00C 8f01C 8f03C 8f05C 8f06C 8f07C 8f0bC 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-EDO / | #5: 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: 1.95 Å3/Da / Density % sol: 36.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 5 uL of 0.6 M Sodium Chloride in 100 mM Sodium Acetate buffer pH 4.5 and 25% ethylene glycol were mixed with 5 uL 100 mg/mL lysozyme in 100 mM Sodium Acetate. |
-Data collection
Diffraction | Mean temperature: 260 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7462 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.781 Å / Num. obs: 9386 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 21.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.019 / Net I/σ(I): 40.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 19.7 / Num. unique obs: 576 / CC1/2: 0.997 / Rpim(I) all: 0.03 / % possible all: 87.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→38.781 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.146 / SU B: 4.91 / SU ML: 0.075 / Average fsc free: 0.9813 / Average fsc work: 0.9894 / Cross valid method: FREE R-VALUE / ESU R: 0.133 / ESU R Free: 0.121 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: 17.462 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→38.781 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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Refinement TLS params. | Method: refined / Origin x: 18.992 Å / Origin y: 40.289 Å / Origin z: -0.46 Å
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Refinement TLS group | Selection: ALL |