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Yorodumi- PDB-8qij: Crystallographic Structure of a Salicylate Synthase from M. absce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qij | ||||||
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Title | Crystallographic Structure of a Salicylate Synthase from M. abscessus (Mab-SaS) | ||||||
Components | Putative anthranilate synthase component I TrpE2/ Salicylate synthase MbtI | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Synthase / Siderophore / Iron Acquisition | ||||||
Function / homology | Function and homology information isochorismate synthase activity / oxo-acid-lyase activity / biosynthetic process Similarity search - Function | ||||||
Biological species | Mycobacteroides abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.073 Å | ||||||
Authors | Cassetta, A. / Covaceuszach, S. / Tomaiuolo, M. / Meneghetti, F. / Villa, S. / Mori, M. / Chiarelli, L.R. / Mangiatordi, G.F. | ||||||
Funding support | Italy, 1items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2024 Title: Structural basis for specific inhibition of salicylate synthase from Mycobacterium abscessus. Authors: Mori, M. / Cocorullo, M. / Tresoldi, A. / Cazzaniga, G. / Gelain, A. / Stelitano, G. / Chiarelli, L.R. / Tomaiuolo, M. / Delre, P. / Mangiatordi, G.F. / Garofalo, M. / Cassetta, A. / ...Authors: Mori, M. / Cocorullo, M. / Tresoldi, A. / Cazzaniga, G. / Gelain, A. / Stelitano, G. / Chiarelli, L.R. / Tomaiuolo, M. / Delre, P. / Mangiatordi, G.F. / Garofalo, M. / Cassetta, A. / Covaceuszach, S. / Villa, S. / Meneghetti, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qij.cif.gz | 336.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qij.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8qij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qij_validation.pdf.gz | 482 KB | Display | wwPDB validaton report |
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Full document | 8qij_full_validation.pdf.gz | 486 KB | Display | |
Data in XML | 8qij_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 8qij_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/8qij ftp://data.pdbj.org/pub/pdb/validation_reports/qi/8qij | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AC
#1: Protein | Mass: 48810.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Residues 1-15 and 453 are missing in the crystallographic model due to the lack of electron density. Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: MAB_2245 / Production host: Escherichia coli (E. coli) / References: UniProt: B1MAQ5 |
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-Non-polymers , 5 types, 359 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.43 Å3/Da / Density % sol: 49.41 % / Description: Thin rods |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 23-27% PEG 3350, 0.15-0.25M ammonium sulphate, 0.1M BIS-TRIS (pH 5.5) PH range: 5.4-5.6 |
-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: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2022 / Details: Pt-coated cylindrical mirror |
Radiation | Monochromator: Double Crystal Si(1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→56.1 Å / Num. obs: 56395 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.057 / Rrim(I) all: 0.195 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.073→2.109 Å / Redundancy: 11.7 % / Rmerge(I) obs: 1.281 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2794 / CC1/2: 0.818 / Rpim(I) all: 0.389 / Rrim(I) all: 1.34 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.073→56.054 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.283 / SU ML: 0.136 / SU R Cruickshank DPI: 0.1967 / Cross valid method: FREE R-VALUE / ESU R: 0.197 / ESU R Free: 0.166 / SU Rfree Cruickshank DPI: 0.166 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.12 Å2
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Refinement step | Cycle: LAST / Resolution: 2.073→56.054 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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