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Yorodumi- PDB-6g8a: Lysozyme solved by Native SAD from a dataset collected in 5 secon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g8a | ||||||
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Title | Lysozyme solved by Native SAD from a dataset collected in 5 seconds at 1 A wavelength with JUNGFRAU detector | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Native-SAD / JUNGFRAU / integrating detector | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / SAD / Resolution: 1.143 Å | ||||||
Authors | Leonarski, F. / Olieric, V. / Vera, L. / Redford, S. / Wang, M. | ||||||
Citation | Journal: Nat. Methods / Year: 2018 Title: Fast and accurate data collection for macromolecular crystallography using the JUNGFRAU detector. Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / ...Authors: Leonarski, F. / Redford, S. / Mozzanica, A. / Lopez-Cuenca, C. / Panepucci, E. / Nass, K. / Ozerov, D. / Vera, L. / Olieric, V. / Buntschu, D. / Schneider, R. / Tinti, G. / Froejdh, E. / Diederichs, K. / Bunk, O. / Schmitt, B. / Wang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g8a.cif.gz | 91.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g8a.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 6g8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/6g8a ftp://data.pdbj.org/pub/pdb/validation_reports/g8/6g8a | HTTPS FTP |
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-Related 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: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 5% PEG MME 5000, 2 M NaCl, 50 mM Sodium Acetate pH 4.5, 25% 480 ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI JUNGFRAU 1M / Detector: PIXEL / Date: Jun 16, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.14→39.45 Å / Num. obs: 77341 / % possible obs: 95.8 % / Redundancy: 15.1 % / Rrim(I) all: 0.037 / Net I/σ(I): 41.82 |
Reflection shell | Resolution: 1.14→1.21 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.95 / Num. unique obs: 9912 / CC1/2: 0.955 / Rrim(I) all: 0.22 / % possible all: 75.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.143→22.262 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 9.84
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Solvent computation | Shrinkage radii: 0.5 Å / VDW probe radii: 0.8 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.143→22.262 Å
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Refine LS restraints |
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LS refinement shell |
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