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Open data
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Basic information
Entry | Database: PDB / ID: 5ej5 | ||||||
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Title | EcMenD-ThDP-Mn2+ complex soaked with 2-ketoglutarate for 1.5 h | ||||||
![]() | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | ||||||
![]() | TRANSFERASE / Post-decarboxylation intermediate | ||||||
Function / homology | ![]() 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase / 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase activity / menaquinone biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / magnesium ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Song, H.G. / Dong, C. / Chen, Y.Z. / Sun, Y.R. / Guo, Z.H. | ||||||
![]() | ![]() Title: A Thiamine-Dependent Enzyme Utilizes an Active Tetrahedral Intermediate in Vitamin K Biosynthesis Authors: Song, H.G. / Dong, C. / Qin, M.M. / Chen, Y.Z. / Sun, Y.R. / Liu, J.J. / Chan, W. / Guo, Z.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 | ![]() | 895.9 KB | Display | ![]() |
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PDB format | ![]() | 734.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 167.2 KB | Display | |
Data in CIF | ![]() | 232.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ej4C ![]() 5ej6C ![]() 5ej7C ![]() 5ej8C ![]() 5ej9C ![]() 5ejaC 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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Unit cell |
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Components
#1: Protein | Mass: 61433.781 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P17109, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase #2: Chemical | ChemComp-TD6 / ( #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.16 M magnesium formate, 1% tascimate pH 7.0, 0.02 M HEPES pH 7.0, 14% PEG 3350 and 2% PEG MME 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.28 Å / Num. obs: 194725 / % possible obs: 92.4 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.8 / % possible all: 95.5 |
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Processing
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Refinement | Resolution: 2.3→33.759 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→33.759 Å
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Refine LS restraints |
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LS refinement shell |
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