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- PDB-4oe7: Crystal structure of YagE, a KDG aldolase protein, in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4oe7 | |||||||||
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Title | Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal | |||||||||
![]() | Probable 2-keto-3-deoxy-galactonate aldolase YagE | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Manoj Kumar, P. / Baskar, V. / Manicka, S. / Krishnaswamy, S. | |||||||||
![]() | ![]() Title: Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal Authors: Manoj Kumar, P. / Baskar, V. / Manicka, S. / Krishnaswamy, S. #1: ![]() Title: Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12. Authors: Manicka, S. / Peleg, Y. / Unger, T. / Albeck, S. / Dym, O. / Greenblatt, H.M. / Bourenkov, G. / Lamzin, V. / Krishnaswamy, S. / Sussman, J.L. #2: ![]() Title: Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis. Authors: Bhaskar, V. / Kumar, M. / Manicka, S. / Tripathi, S. / Venkatraman, A. / Krishnaswamy, S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 245.3 KB | Display | ![]() |
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PDB format | ![]() | 194.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2v8zS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 12 - 309 / Label seq-ID: 30 - 327
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 37013.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P75682, ![]() |
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-Non-polymers , 8 types, 248 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GXT.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/GXP.gif)
![](data/chem/img/GXS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GXT.gif)
![](data/chem/img/PYR.gif)
![](data/chem/img/GXP.gif)
![](data/chem/img/GXS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / ![]() #3: Chemical | ChemComp-GOL / ![]() #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GXT / | ![]() #6: Chemical | ![]() #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.19 % |
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Crystal grow![]() | Temperature: 298 K / Method: microbatch under oil / pH: 6.5 Details: 100mM HEPES pH 6.5, 200mM Magnesium chloride, 15% PEG 3350, MICROBATCH UNDER OIL, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: May 28, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.99→8.89 Å / Num. obs: 83414 / % possible obs: 98.2 % / Redundancy: 4.1 % / Net I/σ(I): 14.43 |
Reflection shell | Resolution: 1.99→2.04 Å / Redundancy: 3.42 % / Mean I/σ(I) obs: 2.76 / % possible all: 87 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2V8Z Resolution: 1.99→49.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.971 / SU ML: 0.111 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.011 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→49.06 Å
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Refine LS restraints |
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