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Yorodumi- PDB-5ej8: EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate fo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ej8 | ||||||
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Title | EcMenD-ThDP-Mn2+ complex structure soaked with 2-ketoglutarate for 2 min | ||||||
Components | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | ||||||
Keywords | TRANSFERASE / Post-decarboxylation intermediate | ||||||
Function / homology | Function and homology information 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 | Escherichia coli K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 Å | ||||||
Authors | Song, H.G. / Dong, C. / Chen, Y.Z. / Sun, Y.R. / Guo, Z.H. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ej8.cif.gz | 2.7 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5ej8.ent.gz | 2.3 MB | Display | PDB format |
PDBx/mmJSON format | 5ej8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ej8_validation.pdf.gz | 984.1 KB | Display | wwPDB validaton report |
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Full document | 5ej8_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5ej8_validation.xml.gz | 213.2 KB | Display | |
Data in CIF | 5ej8_validation.cif.gz | 326.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/5ej8 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/5ej8 | HTTPS FTP |
-Related structure data
Related structure data | 5ej4C 5ej5C 5ej6C 5ej7C 5ej9C 5ejaC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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.) Escherichia coli K12 (bacteria) / Strain: K12 substr. MG1655 / Gene: menD, b2264, JW5374 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) 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 / ( #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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
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 |
-Processing
Software |
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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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