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Yorodumi- PDB-6gi1: Crystal structure of the ferric enterobactin esterase (pfeE) muta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gi1 | ||||||
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Title | Crystal structure of the ferric enterobactin esterase (pfeE) mutant(S157A) from Pseudomonas aeruginosa in presence of enterobactin | ||||||
Components | Ferric enterobactin esterase | ||||||
Keywords | HYDROLASE / PfeE / PA2689 | ||||||
Function / homology | Function and homology information iron(III)-enterobactin esterase / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / periplasmic space Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||
Authors | Moynie, L. / Naismith, J.H. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: A Key Role for the Periplasmic PfeE Esterase in Iron Acquisition via the Siderophore Enterobactin in Pseudomonas aeruginosa. Authors: Perraud, Q. / Moynie, L. / Gasser, V. / Munier, M. / Godet, J. / Hoegy, F. / Mely, Y. / Mislin, G.L.A. / Naismith, J.H. / Schalk, I.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gi1.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gi1.ent.gz | 96.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6gi1 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6gi1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30631.729 Da / Num. of mol.: 2 / Mutation: S157A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA2689 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0F2 |
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-Non-polymers , 6 types, 265 molecules
#2: Chemical | #3: Chemical | ChemComp-DBS / | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-EB4 / | #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: 2.39 Å3/Da / Density % sol: 48.45 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion / Details: PEG MME 2000, Sodium acetate, potassium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→58.55 Å / Num. obs: 70084 / % possible obs: 100 % / Redundancy: 12.61 % / CC1/2: 0.998 / Rmerge(I) obs: 0.1291 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.9 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3440 / CC1/2: 0.525 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→58.55 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.448 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / 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: 37.02 Å2
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Refinement step | Cycle: 1 / Resolution: 1.66→58.55 Å
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Refine LS restraints |
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