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Yorodumi- PDB-4g9s: Crystal structure of Escherichia coli PliG in complex with Atlant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4g9s | ||||||
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Title | Crystal structure of Escherichia coli PliG in complex with Atlantic salmon g-type lysozyme | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / hydrolase inhibitor / lysozyme / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information lysozyme inhibitor activity / peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / periplasmic space / defense response to bacterium / cytosol Similarity search - Function | ||||||
Biological species | Salmo salar (Atlantic salmon) Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å | ||||||
Authors | Leysen, S. / Vanderkelen, L. / Weeks, S.D. / Michiels, C.W. / Strelkov, S.V. | ||||||
Citation | Journal: Cell.Mol.Life Sci. / Year: 2013 Title: Structural basis of bacterial defense against g-type lysozyme-based innate immunity. Authors: Leysen, S. / Vanderkelen, L. / Weeks, S.D. / Michiels, C.W. / Strelkov, S.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g9s.cif.gz | 215.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g9s.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g9/4g9s ftp://data.pdbj.org/pub/pdb/validation_reports/g9/4g9s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 21094.729 Da / Num. of mol.: 1 / Fragment: UNP residues 22-200 / Mutation: A133V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: lysG, LYG / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6PZ97 |
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#2: Protein | Mass: 12538.815 Da / Num. of mol.: 1 / Fragment: UNP residues 23-133 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pliG, ycgK / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76002 |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-FLC / |
#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: 3.07 Å3/Da / Density % sol: 60 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.8M tri-ammonium citrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2012 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 0.95→43.43 Å / Num. obs: 265542 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 | ||||||||||||||||||
Reflection shell | Resolution: 0.95→1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 36278 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MGW AND 4DY3 Resolution: 0.95→43.267 Å / SU ML: 0.12 / σ(F): 1.33 / Phase error: 15.62 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→43.267 Å
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Refine LS restraints |
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LS refinement shell |
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