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- PDB-4kgb: Structure of succinyl-CoA: 3-ketoacid CoA transferase from Drosop... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kgb | ||||||
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Title | Structure of succinyl-CoA: 3-ketoacid CoA transferase from Drosophila melanogaster | ||||||
![]() | Succinyl-CoA:3-ketoacid-coenzyme A transferase | ||||||
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Function / homology | ![]() Utilization of Ketone Bodies / cellular ketone body metabolic process / ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.C. / Shi, Z.B. / Zhang, M. | ||||||
![]() | ![]() Title: Structure of succinyl-CoA:3-ketoacid CoA transferase from Drosophila melanogaster. Authors: Zhang, M. / Xu, H.Y. / Wang, Y.C. / Shi, Z.B. / Zhang, N.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.5 KB | Display | ![]() |
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PDB format | ![]() | 143.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ooyS 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: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 34 - 515 / Label seq-ID: 5 - 486
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Components
#1: Protein | Mass: 51718.457 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 34-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / | ![]() #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.79 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate, 0.1M BIS-TRIS pH 5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.64→50 Å / Num. all: 28659 / Num. obs: 28630 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.65→2.7 Å / Redundancy: 6 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 7 / Num. unique all: 1380 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB code 1OOY Resolution: 2.64→43.34 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.975 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 34.326 Å2
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Refinement step | Cycle: LAST / Resolution: 2.64→43.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 27510 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.644→2.712 Å / Total num. of bins used: 20
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