+Open data
-Basic information
Entry | Database: PDB / ID: 5b48 | ||||||
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Title | 2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai | ||||||
Components | (2-oxoacid--ferredoxin oxidoreductase ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / thiamin pyrophosphate / iron-sulfur cluster / ferredoxin | ||||||
Function / homology | Function and homology information 2-oxobutyrate synthase activity / 2-oxoglutarate synthase activity / 2-oxoacid oxidoreductase (ferredoxin) / pyruvate synthase activity / thiamine pyrophosphate binding / 4 iron, 4 sulfur cluster binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii str. 7 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Yan, Z. / Maruyama, A. / Arakawa, T. / Fushinobu, S. / Wakagi, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2016 Title: Crystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii Authors: Yan, Z. / Maruyama, A. / Arakawa, T. / Fushinobu, S. / Wakagi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b48.cif.gz | 339.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b48.ent.gz | 270.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b48_validation.pdf.gz | 807.6 KB | Display | wwPDB validaton report |
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Full document | 5b48_full_validation.pdf.gz | 841.6 KB | Display | |
Data in XML | 5b48_validation.xml.gz | 57.6 KB | Display | |
Data in CIF | 5b48_validation.cif.gz | 79.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/5b48 ftp://data.pdbj.org/pub/pdb/validation_reports/b4/5b48 | HTTPS FTP |
-Related structure data
Related structure data | 5b46SC 5b47C 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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1 |
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Unit cell |
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-Components
-2-oxoacid--ferredoxin oxidoreductase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 70331.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_23000 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) References: UniProt: Q96Y66, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor #2: Protein | Mass: 33652.621 Da / Num. of mol.: 2 / Mutation: K5T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Strain: 7 / Gene: STK_22980 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) References: UniProt: Q96Y68, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With an iron-sulfur protein as acceptor |
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-Non-polymers , 4 types, 64 molecules
#3: Chemical | ChemComp-SF4 / |
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#4: Chemical | ChemComp-TDN / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.24 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 15% PEG3350, 0.1 M Tris-HCl, 0.1 M NaBr |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 24, 2005 |
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 65171 / % possible obs: 99.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.72 / % possible all: 93.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B46 Resolution: 2.5→36.47 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.974 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 0.651 / ESU R Free: 0.328 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.549 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→36.47 Å
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