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- PDB-5ahs: 3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenell... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ahs | ||||||
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Title | 3-Sulfinopropionyl-Coenzyme A (3SP-CoA) desulfinase from Advenella mimgardefordensis DPN7T: holo crystal structure with the substrate analog succinyl-CoA | ||||||
![]() | ACYL-COA DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 3-sulfinopropanoyl-CoA desulfinase / oxidoreductase activity, acting on the CH-CH group of donors / flavin adenine dinucleotide binding / hydrolase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cianci, M. / Schuermann, M. / Meijers, R. / Schneider, T.R. / Steinbuechel, A. | ||||||
![]() | ![]() Title: 3-Sulfinopropionyl-Coenzyme a (3Sp-Coa) Desulfinase from Advenella Mimigardefordensis Dpn7(T): Crystal Structure and Function of a Desulfinase with an Acyl-Coa Dehydrogenase Fold. Authors: Schurmann, M. / Meijers, R. / Schneider, T.R. / Steinbuchel, A. / Cianci, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 491.6 KB | Display | ![]() |
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PDB format | ![]() | 406.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.1 MB | Display | ![]() |
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Full document | ![]() | 3.1 MB | Display | |
Data in XML | ![]() | 101 KB | Display | |
Data in CIF | ![]() | 137.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5af7SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 43581.746 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET23A / Production host: ![]() ![]() References: UniProt: K4L7X3, 3-sulfinopropanoyl-CoA desulfinase |
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-Non-polymers , 5 types, 1475 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-SIN / | #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55.8 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: CRYSTALS USED FOR X-RAY DIFFRACTION STUDIES WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS- TRIS PH 6.5 AND 5- 20 % ...Details: CRYSTALS USED FOR X-RAY DIFFRACTION STUDIES WERE GROWN IN 24-WELL LINBRO PLATES (HAMPTON RESEARCH) BY VAPOUR DIFFUSION IN A HANGING DROP CONFIGURATION FROM 0.1 M BIS- TRIS PH 6.5 AND 5- 20 % PEG 3350 AT A PROTEIN CONCENTRATION OF 10 MG/ML, BY MIXING 2 UL OF THE PROTEIN SOLUTION WITH 2 UL MOTHER LIQUOR |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2013 / Details: KB MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.968 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→121.29 Å / Num. obs: 126487 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5AF7 Resolution: 2.3→116.746 Å / SU ML: 0.31 / σ(F): 1.91 / Phase error: 27.79 / 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: 2.3→116.746 Å
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Refine LS restraints |
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LS refinement shell |
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