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Yorodumi- PDB-6gi0: Crystal structure of the ferric enterobactin esterase (PfeE) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gi0 | ||||||
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Title | Crystal structure of the ferric enterobactin esterase (PfeE) from Pseudomonas aeruginosa | ||||||
Components | Ferric enterobactin esterase | ||||||
Keywords | HYDROLASE / PfeE / PA2689 | ||||||
Function / homology | iron(III)-enterobactin esterase / Esterase-like / Putative esterase / carboxylic ester hydrolase activity / hydrolase activity, acting on ester bonds / Alpha/Beta hydrolase fold / periplasmic space / NITRATE ION / Iron(III) enterobactin esterase Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6gi0.cif.gz | 211.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gi0.ent.gz | 171.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gi0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/6gi0 ftp://data.pdbj.org/pub/pdb/validation_reports/gi/6gi0 | HTTPS FTP |
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-Related structure data
Related structure data | 6gi1C 6gi2C 6gi5C 2gzrS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 12 - 275 / Label seq-ID: 15 - 278
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-Components
#1: Protein | Mass: 30647.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA2689 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0F2 #2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 35.96 % |
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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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→55.55 Å / Num. obs: 30184 / % possible obs: 96.6 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1755 / CC1/2: 0.93 / % possible all: 75.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2gzr Resolution: 2→55.55 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.557 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.173 / 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: 36.902 Å2
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Refinement step | Cycle: 1 / Resolution: 2→55.55 Å
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Refine LS restraints |
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