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- PDB-8e0x: DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e0x | ||||||||||||||||||
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Title | DAHP (3-deoxy-D-arabinoheptulosonate-7-phosphate) Synthase complexed with Mn(II), PEP, and Pi in unbound:(bound)2:other Conformations | ||||||||||||||||||
![]() | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Berti, P.J. / Junop, M.S. / Grainger, R. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Role of Half-of-Sites Reactivity and Inter-Subunit Communications in DAHP Synthase Catalysis and Regulation. Authors: Balachandran, N. / Grainger, R.A. / Rob, T. / Liuni, P. / Wilson, D.J. / 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 | ![]() | 588.8 KB | Display | ![]() |
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PDB format | ![]() | 463.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8e0sC ![]() 8e0tC ![]() 8e0uC ![]() 8e0vC ![]() 8e0yC ![]() 8e0zC ![]() 5cksS 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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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.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P0AB91, ![]() #2: Chemical | #3: Chemical | ChemComp-PEP / ![]() #4: Chemical | ![]() #5: 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: 50.56 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M trilithium citrate tetrahydrate, 10% (w/v) PEG 3350, 5 mM DAHP oxime, 5 mM phosphoenolpyruvate, 5 mM erythrose 4-pohsphate, 30% (v/v) ethylene glycol, 1:1:0.2 |
-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: Feb 24, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.97→67.65 Å / Num. obs: 105376 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 29.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.03 / Rrim(I) all: 0.058 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.97→2.05 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 5157 / CC1/2: 0.884 / Rpim(I) all: 0.254 / Rrim(I) all: 0.492 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 5CKS Resolution: 1.97→43.48 Å / SU ML: 0.1702 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4764 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: 40.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→43.48 Å
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Refine LS restraints |
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LS refinement shell |
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