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Yorodumi- PDB-6ybf: RT structure of HEW Lysozyme obtained at 1.13 A resolution from c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ybf | ||||||
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Title | RT structure of HEW Lysozyme obtained at 1.13 A resolution from crystal grown in a Kapton microchip. | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / LYSOZYME / 1 / 4-BETA-N-ACETYLMURAMIDASE C | ||||||
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: 1.13 Å | ||||||
Authors | Gavira, J. / Martinez-Rodriguez, S. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Authors: Gavira, J.A. / Rodriguez-Ruiz, I. / Martinez-Rodriguez, S. / Basu, S. / Teychene, S. / McCarthy, A.A. / Mueller-Dieckman, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ybf.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ybf.ent.gz | 54.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ybf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ybf_validation.pdf.gz | 415.4 KB | Display | wwPDB validaton report |
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Full document | 6ybf_full_validation.pdf.gz | 415.4 KB | Display | |
Data in XML | 6ybf_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 6ybf_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/6ybf ftp://data.pdbj.org/pub/pdb/validation_reports/yb/6ybf | HTTPS FTP |
-Related structure data
Related structure data | 6ybiC 6yboC 6ybrC 6ybxC 6yc5C 1ieeS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#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: 1.67 Å3/Da / Density % sol: 26.7 % |
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Crystal grow | Temperature: 293.5 K / Method: counter-diffusion / pH: 4.5 / Details: 5% w/v NaCl, 50 mM AcNa pH 4.5 / PH range: 4.5-4.5 |
-Data collection
Diffraction | Mean temperature: 293.5 K / Ambient temp details: Room Temperature / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 4, 2017 Details: Be CRL lenses for vertical focusing and Rh/Pt/Si coated ellipitcal mirror for horizontal focusing |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→39.55 Å / Num. obs: 44967 / % possible obs: 98.12 % / Redundancy: 11.56 % / Biso Wilson estimate: 16.46 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.13→1.17 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3710 / CC1/2: 0.7 / % possible all: 82.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IEE Resolution: 1.13→39.55 Å / SU ML: 0.0912 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.1622
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.17 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.13→39.55 Å
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Refine LS restraints |
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LS refinement shell |
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