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- PDB-5e3q: Crystal structure of DapD in complex with succinyl-CoA from Coryn... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5e3q | ||||||
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Title | Crystal structure of DapD in complex with succinyl-CoA from Corynebacterium glutamicum | ||||||
![]() | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | ||||||
![]() | TRANSFERASE / Corynebacterium glutamicum / L-lysine | ||||||
Function / homology | ![]() 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sagong, H.-Y. / Kim, K.-J. | ||||||
![]() | ![]() Title: Crystal Structure and Biochemical Characterization of Tetrahydrodipicolinate N-Succinyltransferase from Corynebacterium glutamicum. Authors: Sagong, H.Y. / Kim, K.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 | ![]() | 75.2 KB | Display | ![]() |
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PDB format | ![]() | 53 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 670.9 KB | Display | ![]() |
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Full document | ![]() | 676.6 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e3pC ![]() 5e3rC ![]() 3fsxS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31909.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 Gene: dapD, Cgl1106, cg1256 / Plasmid: pET30a / Production host: ![]() ![]() References: UniProt: Q8NRE3, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
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#2: Chemical | ChemComp-SCA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.97 Å3/Da / Density % sol: 69.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 200, Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2015 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→94.11 Å / Num. obs: 41214 / % possible obs: 99.17 % / Redundancy: 10.5 % / Net I/σ(I): 61.68 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3FSX Resolution: 1.8→94.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.455 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.082 / 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 max: 82.86 Å2 / Biso mean: 23.175 Å2 / Biso min: 9.91 Å2
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Refinement step | Cycle: final / Resolution: 1.8→94.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.799→1.845 Å / Total num. of bins used: 20
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