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Yorodumi- PDB-5uxf: Crystal Structure of mouse RECON (AKR1C13) in complex with Cyclic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5uxf | ||||||
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Title | Crystal Structure of mouse RECON (AKR1C13) in complex with Cyclic di-AMP | ||||||
Components | Dihydrodiol dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / Cyclic di-AMP / Aldo-keto reductase / TIM barrel | ||||||
Function / homology | Function and homology information steroid dehydrogenase activity / ketosteroid monooxygenase activity / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / aldose reductase (NADPH) activity / steroid metabolic process / xenobiotic metabolic process / oxidoreductase activity / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.501 Å | ||||||
Authors | Luo, S. / Tong, L. | ||||||
Citation | Journal: Immunity / Year: 2017 Title: Sensing of Bacterial Cyclic Dinucleotides by the Oxidoreductase RECON Promotes NF-kappa B Activation and Shapes a Proinflammatory Antibacterial State. Authors: McFarland, A.P. / Luo, S. / Ahmed-Qadri, F. / Zuck, M. / Thayer, E.F. / Goo, Y.A. / Hybiske, K. / Tong, L. / Woodward, J.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uxf.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uxf.ent.gz | 65.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uxf_validation.pdf.gz | 719.3 KB | Display | wwPDB validaton report |
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Full document | 5uxf_full_validation.pdf.gz | 720.4 KB | Display | |
Data in XML | 5uxf_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 5uxf_validation.cif.gz | 27.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/5uxf ftp://data.pdbj.org/pub/pdb/validation_reports/ux/5uxf | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 39291.031 Da / Num. of mol.: 1 / Fragment: RECON / Mutation: K68A, K70A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Akr1c13, ddh / Plasmid: pSpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q54A37, UniProt: Q8VC28*PLUS |
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#2: Chemical | ChemComp-2BA / ( |
#3: 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: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2 M NaCl, 0.1 M Bis-Tris, pH5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→25 Å / Num. obs: 52009 / % possible obs: 98.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 13.06 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Χ2: 1.043 / Net I/σ(I): 18.1 / Num. measured all: 295963 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Resolution: 1.501→24.182 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.31 Å2 / Biso mean: 17.2153 Å2 / Biso min: 6.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.501→24.182 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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