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Yorodumi- PDB-6w7p: Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment -
+Open data
-Basic information
Entry | Database: PDB / ID: 6w7p | ||||||
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Title | Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / ANTIMICROBIAL PROTEIN / muramidase | ||||||
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 / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Fernandez, D. / Russi, S. | ||||||
Citation | Journal: NPJ Microgravity / Year: 2020 Title: Protein structural changes on a CubeSat under rocket acceleration profile. Authors: Luna, A. / Meisel, J. / Hsu, K. / Russi, S. / Fernandez, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6w7p.cif.gz | 45.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6w7p.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 6w7p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/6w7p ftp://data.pdbj.org/pub/pdb/validation_reports/w7/6w7p | HTTPS FTP |
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-Related structure data
Related structure data | 6w8eC 5kxkS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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: B8YK79, UniProt: P00698*PLUS, lysozyme | ||||
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#2: Chemical | ChemComp-NA / | ||||
#3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 296 K / Method: liquid diffusion / pH: 4.6 / Details: PEG 6000, NaCl, Na Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2019 Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.19499 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.6→55.767 Å / Num. obs: 15331 / % possible obs: 96.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.7 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 9.9 / Net I/σ(I): 10.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5kxk Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.084 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.103 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.37 Å2 / Biso mean: 28.344 Å2 / Biso min: 16.54 Å2
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Refinement step | Cycle: final / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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