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- PDB-8gek: Dihydrodipicolinate synthase with pyruvate from Candidatus Liberi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8gek | ||||||
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Title | Dihydrodipicolinate synthase with pyruvate from Candidatus Liberibacter solanacearum | ||||||
![]() | 4-hydroxy-tetrahydrodipicolinate synthase | ||||||
![]() | LYASE / TIM Barrel | ||||||
Function / homology | ![]() (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.J. | ||||||
Funding support | 1items
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![]() | ![]() Title: Dihydrodipicolinate synthase with pyruvate from the plant pathogen, Candidatus Liberibacter solanacearum Authors: Gilkes, J.M. / Frampton, R.A. / Board, A. / Sheen, C.R. / Smith, G.R. / Dobson, R.C.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 | ![]() | 636.8 KB | Display | ![]() |
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PDB format | ![]() | 535.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.9 KB | Display | ![]() |
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Full document | ![]() | 483 KB | Display | |
Data in XML | ![]() | 70.9 KB | Display | |
Data in CIF | ![]() | 101.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7loyC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 32038.242 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dapA / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Crystallization trials used the sitting drop vapour diffusion method, at 20 C, with droplets consisting of 150 nL of protein solution and 150 nL of reservoir solution. Rectangular CLsoDHDPS ...Details: Crystallization trials used the sitting drop vapour diffusion method, at 20 C, with droplets consisting of 150 nL of protein solution and 150 nL of reservoir solution. Rectangular CLsoDHDPS crystals were produced using the JCSG+ Suite screen in condition A2 (20% w/v polyethylene glycol 3000, 0.1 M sodium citrate, pH 5.5). For ligand bound structures, the crystals were soaked for 7 days in mother liquor with either: 100 mM lysine, 100 mM pyruvate or 100 mM of both succinic semi-aldehyde and pyruvate. |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→45.81 Å / Num. obs: 151510 / % possible obs: 99.5 % / Redundancy: 3.94 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.93→1.96 Å / Num. unique obs: 6831 / CC1/2: 0.468 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→45.81 Å
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Refine LS restraints |
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LS refinement shell |
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