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Yorodumi- PDB-6h79: SSX structure of Lysozyme in flow - metal-kapton microfluidic device -
+Open data
-Basic information
Entry | Database: PDB / ID: 6h79 | |||||||||
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Title | SSX structure of Lysozyme in flow - metal-kapton microfluidic device | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Monteiro, D.C.F. / Trebbin, M. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: J.Synchrotron Radiat. / Year: 2019 Title: A microfluidic flow-focusing device for low sample consumption serial synchrotron crystallography experiments in liquid flow. Authors: Monteiro, D.C.F. / Vakili, M. / Harich, J. / Sztucki, M. / Meier, S.M. / Horrell, S. / Josts, I. / Trebbin, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6h79.cif.gz | 41.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6h79.ent.gz | 27.1 KB | Display | PDB format |
PDBx/mmJSON format | 6h79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/6h79 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/6h79 | HTTPS FTP |
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-Related structure data
Related structure data | 5mjjS S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 36 molecules
#2: Chemical | ChemComp-CL / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-EDO / |
#5: Chemical | ChemComp-NA / |
#6: 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: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | Temperature: 275 K / Method: batch mode / pH: 3.5 Details: 3:1 v/v precipitant solution:protein solution precipitant: 50 mM NaAc pH 3.5, 1M NaCl, 35% ethylene glycol, 20% PEG3350 protein buffer: 50 mM NaAc (pH 3.5) |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.954 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.954 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→56.07 Å / Num. obs: 7013 / % possible obs: 100 % / Redundancy: 121.1 % / Biso Wilson estimate: 52.38 Å2 / CC1/2: 0.96 / R split: 0.1158 / Net I/σ(I): 5.57 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 87.6 % / Mean I/σ(I) obs: 1.36 / CC1/2: 0.32 / R split: 1.13 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MJJ Resolution: 2.1→56.07 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.957 / SU B: 6.127 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 49.631 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→56.07 Å
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Refine LS restraints |
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