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Open data
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Basic information
Entry | Database: PDB / ID: 7rue | |||||||||||||||
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Title | DAHP synthase complexed with trifluoropyruvate semicarbazone | |||||||||||||||
![]() | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive | |||||||||||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / DAHP synthase / inhibitor complex / LYASE / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||||||||
Function / homology | ![]() 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Heimhalt, M. / Mukherjee, P. / Grainger, R. / Szabla, R. / Brown, C. / Turner, R. / Junop, M.S. / Berti, P.J. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: An Inhibitor-in-Pieces Approach to DAHP Synthase Inhibition: Potent Enzyme and Bacterial Growth Inhibition. Authors: Heimhalt, M. / Mukherjee, P. / Grainger, R.A. / Szabla, R. / Brown, C. / Turner, R. / Junop, M.S. / Berti, P.J. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 286.5 KB | Display | ![]() |
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PDB format | ![]() | 211.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 50.3 KB | Display | |
Data in CIF | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rudC ![]() 5cksS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 38116.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: aroG, b0754, JW0737 / Production host: ![]() ![]() References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-7QH / ( #3: Chemical | ChemComp-MN / #4: 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: 2.49 Å3/Da / Density % sol: 50.52 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M trilithium citrate tetrahydrate 20% (w/v) PEG 3350 1 M MnCl2 2 mM trifluoropyruvate semicarbazone |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→72.02 Å / Num. obs: 52544 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.23 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.073 / Rrim(I) all: 0.133 / Net I/av σ(I): 6.8 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4524 / CC1/2: 0.801 / Rpim(I) all: 0.397 / Rrim(I) all: 0.329 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5cks Resolution: 2.5→50.21 Å / SU ML: 0.3719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.7414 / Stereochemistry target values: GeoStd + Monomer Library
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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: 43.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→50.21 Å
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Refine LS restraints |
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LS refinement shell |
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