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Yorodumi- PDB-6ba9: YbtT - Type II thioesterase from Yersiniabactin NRPS/PKS biosynth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ba9 | |||||||||
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Title | YbtT - Type II thioesterase from Yersiniabactin NRPS/PKS biosynthetic pathway- S89A mutant | |||||||||
Components | Iron aquisition yersiniabactin synthesis enzyme, YbtT | |||||||||
Keywords | HYDROLASE / Thioesterase / non-ribosomal peptide synthesis / sideraphore synthesis / yersiniabactin | |||||||||
Function / homology | Thioesterase type II, NRPS/PKS/S-FAS / Hydrolases; Acting on ester bonds; Thioester hydrolases / Thioesterase / Thioesterase domain / biosynthetic process / Alpha/Beta hydrolase fold / hydrolase activity / Siderophore biosynthesis thioesterase Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Brett, T.J. / Kober, D.L. / Ohlemacher, S.I. / Henderson, J.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2018 Title: YbtT is a low-specificity type II thioesterase that maintains production of the metallophore yersiniabactin in pathogenic enterobacteria. Authors: Ohlemacher, S.I. / Xu, Y. / Kober, D.L. / Malik, M. / Nix, J.C. / Brett, T.J. / Henderson, J.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ba9.cif.gz | 109 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ba9.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ba9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ba/6ba9 ftp://data.pdbj.org/pub/pdb/validation_reports/ba/6ba9 | HTTPS FTP |
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-Related structure data
Related structure data | 6ba8C 3qmwS C: citing same article (ref.) 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
#1: Protein | Mass: 29395.311 Da / Num. of mol.: 1 / Mutation: S89A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: irp4, srfAD, A4T40_14730, AML07_28155, AUS26_21405, AW106_20985, ECONIH1_11380, ERS085406_04094, ERS150876_03959, FORC28_2175, MS6198_22290, SK85_02209, WM48_10340 Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 DE3 References: UniProt: A0A061LQM0, Hydrolases; Acting on ester bonds; Thioester hydrolases |
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#2: 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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: 200 mM di-ammonium hydrogen citrate, 21% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jun 2, 2017 |
Radiation | Monochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→58.3 Å / Num. obs: 55628 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 16.8 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 5 % / Rmerge(I) obs: 1.865 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2396 / CC1/2: 0.303 / Rpim(I) all: 1.109 / Rrim(I) all: 2.077 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3QMW Resolution: 1.4→47.524 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→47.524 Å
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Refine LS restraints |
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LS refinement shell |
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