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- PDB-8h8u: Room-temperature structure of lysozyme by pink-beam serial crysta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8h8u | ||||||||||||
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Title | Room-temperature structure of lysozyme by pink-beam serial crystallography (50 ms, center) | ||||||||||||
![]() | Lysozyme C | ||||||||||||
![]() | HYDROLASE / pink-beam / serial synchrotron crystallography / room-temperature | ||||||||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Kim, Y. / Nam, K.H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Data of pink-beam serial synchrotron crystallography at the Pohang Light Source II. Authors: Kim, Y. / Nam, K.H. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.9 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.3 KB | Display | ![]() |
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Full document | ![]() | 435.2 KB | Display | |
Data in XML | ![]() | 8.3 KB | Display | |
Data in CIF | ![]() | 10.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h8tC ![]() 8h8vC ![]() 8h8wC ![]() 7wucS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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) ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 299.5 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 28, 2022 |
Radiation | Monochromator: Mo/B4C multilayer, 1.2 % BW / 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: 551.7 % / CC1/2: 0.9881 / Net I/σ(I): 6.13 |
Reflection shell | Resolution: 1.7→1.76 Å / Num. unique obs: 1380 / CC1/2: 0.4314 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7WUC Resolution: 1.7→55.78 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.08 / 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: 62.94 Å2 / Biso mean: 21.78 Å2 / Biso min: 8.83 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: 7
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