+Open data
-Basic information
Entry | Database: PDB / ID: 6mx9 | |||||||||
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Title | Lysozyme bound to 3-Aminophenol | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / nucleation / lysozyme / drug discovery | |||||||||
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: 1.35 Å | |||||||||
Authors | Blackburn, A. / Partowmah, S.H. / Brennan, H.M. / Mestizo, K.E. / Stivala, C.D. / Petreczky, J. / Perez, A. / Horn, A. / McSweeney, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: A simple technique to improve microcrystals using gel exclusion of nucleation inducing elements Authors: Blackburn, A. / Partowmah, S.H. / Brennan, H.M. / Mestizo, K.E. / Stivala, C.D. / Petreczky, J. / Perez, A. / Horn, A. / McSweeney, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mx9.cif.gz | 51.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mx9.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 6mx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/6mx9 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/6mx9 | HTTPS FTP |
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-Related structure data
Related structure data | 6msxC 4n8zS 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
-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, 229 molecules
#2: Chemical | ChemComp-EDO / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-BEN / | #6: Chemical | #7: 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: 2.08 Å3/Da / Density % sol: 40.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 10uL of 50mM 3-aminophenol was deposited on a cover slip and allowed to dry. A 20 uL pellet of 4% sodium chloride + 5% ethylene glycol + 10% glycerol in 2% agar was deposited on the cover ...Details: 10uL of 50mM 3-aminophenol was deposited on a cover slip and allowed to dry. A 20 uL pellet of 4% sodium chloride + 5% ethylene glycol + 10% glycerol in 2% agar was deposited on the cover slip. Adjacent to this was positioned lysozyme (10 ul of 30 mg/ml lysozyme in 100 mM sodium acetate pH 4.6). The cover slip was equilibrated over precipitant containing all the crystallization components. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→28.31 Å / Num. obs: 25655 / % possible obs: 99.7 % / Redundancy: 12.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 3.2 / CC1/2: 0.906 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4N8Z Resolution: 1.35→28.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.85 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.059 / 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: 18.817 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→28.31 Å
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Refine LS restraints |
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