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Yorodumi- PDB-7tz4: Salicylate Adenylate PchD from Pseudomonas aeruginosa containing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tz4 | ||||||||||||
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Title | Salicylate Adenylate PchD from Pseudomonas aeruginosa containing 4-cyanosalicyl-AMS | ||||||||||||
Components | Pyochelin biosynthesis salicyl-AMP ligase PchD | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / adenylate syntase / salicylate | ||||||||||||
Function / homology | Function and homology information ligase activity / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases Similarity search - Function | ||||||||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||||||||
Authors | Shelton, C.L. / Meneely, K.M. / Lamb, A.L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Biol.Inorg.Chem. / Year: 2022 Title: Rational inhibitor design for Pseudomonas aeruginosa salicylate adenylation enzyme PchD. Authors: Shelton, C.L. / Meneely, K.M. / Ronnebaum, T.A. / Chilton, A.S. / Riley, A.P. / Prisinzano, T.E. / Lamb, A.L. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tz4.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tz4.ent.gz | 166.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tz/7tz4 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tz4 | HTTPS FTP |
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-Related structure data
Related structure data | 7tybSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 59982.332 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pchD, LYSZa2_15910, LYSZa5_15910 / Production host: Escherichia coli (E. coli) References: UniProt: A0A8A4FQG3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-KUX / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M ammonium acetate, 0.1 M MES pH 5.6, 0.03 M ammonium chloride, 26% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2016 Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→36.93 Å / Num. obs: 56335 / % possible obs: 97.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 13.56 Å2 / Rpim(I) all: 0.062 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.69→1.72 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 2309 / Rpim(I) all: 0.526 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TYB Resolution: 1.69→36.93 Å / SU ML: 0.1525 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.3318 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→36.93 Å
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Refine LS restraints |
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LS refinement shell |
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