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Yorodumi- PDB-8f28: Lysozyme Structures from Single-Entity Crystallization Method NanoAC -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f28 | ||||||
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Title | Lysozyme Structures from Single-Entity Crystallization Method NanoAC | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / ACT binding | ||||||
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: 1.2 Å | ||||||
Authors | Yang, R. / Sankaran, B. / Ogbonna, E. / Wang, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Anal.Chem. / Year: 2023 Title: A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis. Authors: Yang, R. / Kvetny, M. / Brown, W. / Ogbonna, E.N. / Wang, G. #1: Journal: Anal. Chem. / Year: 2023 Title: Lysozyme Structures from Single-Entity Crystallization Method NanoAC Authors: Yang, R. / Sankaran, B. / Ogbonna, E. / Wang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f28.cif.gz | 86.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f28.ent.gz | 53.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f28_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 8f28_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 8f28_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 8f28_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/8f28 ftp://data.pdbj.org/pub/pdb/validation_reports/f2/8f28 | HTTPS FTP |
-Related structure data
Related structure data | 1ieeS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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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 / Fragment: lyzozyme / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #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: 1.98 Å3/Da / Density % sol: 37.99 % / Description: tetragonal |
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Crystal grow | Temperature: 295 K / Method: liquid diffusion / pH: 4.8 Details: A new crystallization method named NanoAC was used. Protein solution and precipitant solution were connected through a single nanopipette to control (in time and space) nucleation and crystal growth |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 6, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double-crystal Si(111) and multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 35301 / % possible obs: 96.4 % / Redundancy: 7 % / Biso Wilson estimate: 10.32 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.028 / Rrim(I) all: 0.079 / Χ2: 3.799 / Net I/σ(I): 20.1 / Num. measured all: 246464 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1iee Resolution: 1.2→30.69 Å / SU ML: 0.0923 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.1154 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→30.69 Å
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Refine LS restraints |
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LS refinement shell |
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