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Yorodumi- PDB-5af7: 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenell... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5af7 | ||||||
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Title | 3-Sulfinopropionyl-coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis DPN7T: crystal structure and function of a desulfinase with an acyl-CoA dehydrogenase fold. Native crystal structure | ||||||
Components | ACYL-COA DEHYDROGENASE | ||||||
Keywords | HYDROLASE / DESULFINASE / ACYL-COA DEHYDROGENASE / 3-SULFINOPROPIONYL-COENZYME A / FLAVIN ADENINE DINUCLEOTIDE | ||||||
Function / homology | Function and homology information 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 | Advenella mimigardefordensis DPN7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Cianci, M. / Schuermann, M. / Meijers, R. / Schneider, T.R. / Steinbuechel, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5af7.cif.gz | 182.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5af7.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 5af7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5af7_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5af7_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5af7_validation.xml.gz | 39.4 KB | Display | |
Data in CIF | 5af7_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5af7 ftp://data.pdbj.org/pub/pdb/validation_reports/af/5af7 | HTTPS FTP |
-Related structure data
Related structure data | 5ahsC 1ukwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 43581.746 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Advenella mimigardefordensis DPN7 (bacteria) Plasmid: PET23A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: K4L7X3, 3-sulfinopropanoyl-CoA desulfinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.4 Details: THE CRYSTALS 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 10 % PEG 3350 AT A PROTEIN ...Details: THE CRYSTALS 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 10 % 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: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.968 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 17, 2012 |
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: 1.89→100.65 Å / Num. obs: 69785 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Biso Wilson estimate: 19.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.89→1.93 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UKW Resolution: 1.89→63.79 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.94 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→63.79 Å
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Refine LS restraints |
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LS refinement shell |
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