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Yorodumi- PDB-7tyb: Salicylate Adenylate PchD from Pseudomonas aeruginosa containing ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tyb | ||||||||||||
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Title | Salicylate Adenylate PchD from Pseudomonas aeruginosa containing salicyl-AMS | ||||||||||||
Components | Pyochelin biosynthesis protein PchD | ||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / siderophore | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||||||||
Authors | Meneely, K.M. / Shelton, C.L. / 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 | 7tyb.cif.gz | 251.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tyb.ent.gz | 164.9 KB | Display | PDB format |
PDBx/mmJSON format | 7tyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tyb_validation.pdf.gz | 778.7 KB | Display | wwPDB validaton report |
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Full document | 7tyb_full_validation.pdf.gz | 785.5 KB | Display | |
Data in XML | 7tyb_validation.xml.gz | 22.3 KB | Display | |
Data in CIF | 7tyb_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ty/7tyb ftp://data.pdbj.org/pub/pdb/validation_reports/ty/7tyb | HTTPS FTP |
-Related structure data
Related structure data | 7tz4C 1mdbS 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 PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: pchD, PA4228 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9HWG3 |
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#2: Chemical | ChemComp-KT0 / |
#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: 2.2 Å3/Da / Density % sol: 43.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.2 M ammonium acetate, 0.1 M MES pH 5.4, 0.03 M ammonium chloride, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 23, 2016 / Details: Mirror: Rh coated flat bent mirror |
Radiation | Monochromator: Si(111) side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→39.48 Å / Num. obs: 29938 / % possible obs: 99.1 % / Redundancy: 5.5 % / Biso Wilson estimate: 17.06 Å2 / Rpim(I) all: 0.091 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.11→2.18 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2235 / Rpim(I) all: 0.426 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MDB Resolution: 2.11→37.01 Å / SU ML: 0.2384 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.5111 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.99 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→37.01 Å
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Refine LS restraints |
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LS refinement shell |
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