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- PDB-7x17: Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala -
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Open data
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Basic information
Entry | Database: PDB / ID: 7x17 | ||||||
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Title | Structure of Pseudomonas NRPS protein, AmbB-TC bound to Ppant-L-Ala | ||||||
![]() | AMB antimetabolite synthase AmbB | ||||||
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Function / homology | ![]() L-alanine-[L-alanyl-carrier protein] ligase / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | ChuYuanKee, M. / Bharath, S.R. / Song, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural insights into the substrate-bound condensation domains of non-ribosomal peptide synthetase AmbB. Authors: Chu Yuan Kee, M.J. / Bharath, S.R. / Wee, S. / Bowler, M.W. / Gunaratne, J. / Pan, S. / Zhang, L. / Song, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426.5 KB | Display | ![]() |
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PDB format | ![]() | 278 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7x0eSC ![]() 7x0fC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55970.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: Q9I1H0, L-alanine-[L-alanyl-carrier protein] ligase #2: Chemical | ChemComp-868 / #3: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion Details: 0.1M MES pH 6.6, 0.2M ammonium nitrate, 15% PEG 3350, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Mar 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→48.83 Å / Num. obs: 78940 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 24.52 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.5→2.55 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4499 / CC1/2: 0.559 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7X0E Resolution: 2.5→46.59 Å / SU ML: 0.3807 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8858 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: 29.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→46.59 Å
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Refine LS restraints |
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LS refinement shell |
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