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- PDB-5ej8: EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate fo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ej8 | ||||||
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Title | EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min | ||||||
![]() | 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 | ![]() | 2.7 MB | Display | ![]() |
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PDB format | ![]() | 2.3 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 984.1 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 213.2 KB | Display | |
Data in CIF | ![]() | 326.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ej4C ![]() 5ej5C ![]() 5ej6C ![]() 5ej7C ![]() 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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1 | ![]()
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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
-Protein , 1 types, 8 molecules ABCDEFGH
#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 |
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-Non-polymers , 8 types, 5788 molecules 














#2: Chemical | ChemComp-TD6 / ( |
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#3: Chemical | ChemComp-MN / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-GOL / |
#6: Chemical | ChemComp-EDO / |
#7: Chemical | ChemComp-FMT / |
#8: Chemical | ChemComp-TRS / |
#9: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.39 % |
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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: Apr 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→27.65 Å / Num. obs: 1002427 / % possible obs: 94.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2 / % possible all: 92.4 |
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Processing
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Refinement | Resolution: 1.34→27.649 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.52 / 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: 1.34→27.649 Å
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Refine LS restraints |
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LS refinement shell |
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