+Open data
-Basic information
Entry | Database: PDB / ID: 6agr | ||||||
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Title | Structure of HEWL co-crystallised with phenylethyl alcohol | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / HEWL / phenylethyl alcohol | ||||||
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: 1.22 Å | ||||||
Authors | Seyedarabi, A. / Seraj, Z. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2019 Title: The role of Cinnamaldehyde and Phenyl ethyl alcohol as two types of precipitants affecting protein hydration levels. Authors: Seraj, Z. / Seyedarabi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6agr.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6agr.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 6agr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6agr ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6agr | HTTPS FTP |
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-Related structure data
Related structure data | 6abzC 6agnC 1dpxS C: citing same article (ref.) 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 , 6 types, 218 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEL / | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.78 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 2M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→55.52 Å / Num. obs: 34989 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 1.22→1.28 Å / Rmerge(I) obs: 0.392 / Num. unique obs: 4996 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DPX Resolution: 1.22→55.52 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 0.614 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.044 / 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: 15.38 Å2
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Refinement step | Cycle: 1 / Resolution: 1.22→55.52 Å
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Refine LS restraints |
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