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- PDB-8e0v: 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: 8e0v | ||||||||||||||||||
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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 | ||||||||||||||||||
![]() | LYASE / DAHP synthase inhibitor / DAHP oxime 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 / cytosol / cytoplasm 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 | ![]() | 571.3 KB | Display | ![]() |
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PDB format | ![]() | 448.2 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 ![]() 8e0xC ![]() 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
-Protein / Sugars , 2 types, 7 molecules ABCD![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#1: Protein | Mass: 38116.555 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0AB91, 3-deoxy-7-phosphoheptulonate synthase #3: Sugar | |
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-Non-polymers , 4 types, 933 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/PEP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEP.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.25 % |
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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 erythrose 4-phosphate, 5 mM phosphoenolpyruvate, 30% (w/v) D-(+)-galactose |
-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: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→64.45 Å / Num. obs: 66903 / % possible obs: 96.1 % / Observed criterion σ(F): 1.35 / Redundancy: 3.7 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.047 / Rrim(I) all: 0.091 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 4452 / CC1/2: 0.883 / Rpim(I) all: 0.241 / Rrim(I) all: 0.461 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CKS Resolution: 2.3→49.65 Å / SU ML: 0.2247 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.457 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: 28.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→49.65 Å
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Refine LS restraints |
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LS refinement shell |
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