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Yorodumi- PDB-6k5q: Crystal structure of lysozyme complexed with a bioactive compound... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k5q | ||||||
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Title | Crystal structure of lysozyme complexed with a bioactive compound from Jatropha gossypiifolia | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Lysozyme / Jatropha gossypifolia | ||||||
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: 1.177 Å | ||||||
Authors | Kanal Elamparithi, B. / Ankur, T. / Sivakumar, M. / Gunasekaran, K. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of lysozyme complexed with a bioactive compound from Jatropha gossypiifolia Authors: Kanal Elamparithi, B. / Ankur, T. / Sivakumar, M. / Gunasekaran, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k5q.cif.gz | 71.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k5q.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 6k5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k5/6k5q ftp://data.pdbj.org/pub/pdb/validation_reports/k5/6k5q | HTTPS FTP |
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-Related structure data
Related structure data | 2lymS 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 genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme |
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-Non-polymers , 5 types, 138 molecules
#2: Chemical | ChemComp-ACT / |
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#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-NA / |
#5: Chemical | ChemComp-D2L / [( |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 100mM Sodium Acetate pH 4.5, 20% (v/v) Ethylene Glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.999995 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999995 Å / Relative weight: 1 |
Reflection | Resolution: 1.1767→34.552 Å / Num. obs: 38548 / % possible obs: 98.4 % / Redundancy: 3.51 % / Biso Wilson estimate: 10.2 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.04 / Net I/av σ(I): 5.28 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.1767→1.25 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 2.38 / Num. unique obs: 11537 / CC1/2: 0.89 / Rrim(I) all: 0.52 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2LYM Resolution: 1.177→34.552 Å / SU ML: 0.13 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 21.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.87 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.177→34.552 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 0.8965 Å / Origin y: -19.9098 Å / Origin z: 0.4285 Å
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Refinement TLS group | Selection details: all |