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Yorodumi- PDB-8h8w: Room-temperature structure of lysozyme by pink-beam serial crysta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h8w | ||||||||||||
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Title | Room-temperature structure of lysozyme by pink-beam serial crystallography (100 ms, center) | ||||||||||||
Components | Lysozyme C | ||||||||||||
Keywords | HYDROLASE / serial crystallography / pink-beam / serial synchrotron crystallography / room-temperature | ||||||||||||
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: 1.7 Å | ||||||||||||
Authors | Kim, Y. / Nam, K.H. | ||||||||||||
Funding support | Korea, Republic Of, 3items
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Citation | Journal: Data Brief / Year: 2024 Title: Data of pink-beam serial synchrotron crystallography at the Pohang Light Source II. Authors: Kim, Y. / Nam, K.H. #1: Journal: Crystals / Year: 2022 Title: Pink-Beam Serial Synchrotron Crystallography at Pohang Light Source II Authors: Kim, Y. / Nam, K.H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h8w.cif.gz | 43.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h8w.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 8h8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8h8w_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 8h8w_full_validation.pdf.gz | 439.8 KB | Display | |
Data in XML | 8h8w_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 8h8w_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/8h8w ftp://data.pdbj.org/pub/pdb/validation_reports/h8/8h8w | HTTPS FTP |
-Related structure data
Related structure data | 8h8tC 8h8uC 8h8vC 7wucS 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 / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: 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: 40.44 % |
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Crystal grow | Temperature: 298.5 K / Method: small tubes / Details: Na-acetate, NaCl, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 299.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.8009 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2022 |
Radiation | Monochromator: Mo/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8009 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→80.6 Å / Num. obs: 14189 / % possible obs: 100 % / Redundancy: 830 % / CC1/2: 0.9876 / Net I/σ(I): 6.51 |
Reflection shell | Resolution: 1.7→1.76 Å / Num. unique obs: 1380 / CC1/2: 0.5542 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7WUC Resolution: 1.7→55.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.11 / Stereochemistry target values: ML
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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 max: 52.22 Å2 / Biso mean: 20.4717 Å2 / Biso min: 7.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→55.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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