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- PDB-5uxf: Crystal Structure of mouse RECON (AKR1C13) in complex with Cyclic... -

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Basic information

Entry
Database: PDB / ID: 5uxf
TitleCrystal Structure of mouse RECON (AKR1C13) in complex with Cyclic di-AMP
ComponentsDihydrodiol dehydrogenase
KeywordsOXIDOREDUCTASE / 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
Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel ...Aldo-keto reductase family 1 member C / Aldo/keto reductase family signature 1. / NADP-dependent oxidoreductase domain / Aldo/keto reductase family signature 2. / Aldo/keto reductase, conserved site / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / Dihydrodiol dehydrogenase / Aldo-keto reductase family 1 member C13
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.501 Å
AuthorsLuo, S. / Tong, L.
CitationJournal: 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
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrodiol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9492
Polymers39,2911
Non-polymers6581
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.644, 75.422, 88.416
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Dihydrodiol dehydrogenase


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
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5530.2420.9250.1590.2911.0992.7
1.55-1.623.90.2070.950.1180.2391.07399.1
1.62-1.695.70.1820.9760.0820.21.051100
1.69-1.786.40.1480.9860.0630.1611.012100
1.78-1.896.40.1240.990.0530.1351.032100
1.89-2.046.40.1020.9910.0440.1111.032100
2.04-2.246.40.0880.9930.0370.0951.041100
2.24-2.566.40.0790.9940.0340.0860.998100
2.56-3.236.30.0760.9940.0330.0831.082100
3.23-255.70.0580.9950.0260.0641.06897.2

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.501→24.182 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.13
RfactorNum. reflection% reflection
Rfree0.1861 2623 5.05 %
Rwork0.1679 --
obs0.1688 51925 98.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 51.31 Å2 / Biso mean: 17.2153 Å2 / Biso min: 6.68 Å2
Refinement stepCycle: final / Resolution: 1.501→24.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 44 432 3002
Biso mean--14.23 26.78 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062631
X-RAY DIFFRACTIONf_angle_d0.9773570
X-RAY DIFFRACTIONf_chiral_restr0.057393
X-RAY DIFFRACTIONf_plane_restr0.006454
X-RAY DIFFRACTIONf_dihedral_angle_d14.7911600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5014-1.52860.20421170.1812203232085
1.5286-1.5580.19451320.17222459259196
1.558-1.58980.19851340.16272537267198
1.5898-1.62440.2111400.164226162756100
1.6244-1.66220.17451380.157826002738100
1.6622-1.70370.18461380.159326022740100
1.7037-1.74980.15351390.16126112750100
1.7498-1.80130.18691400.165626332773100
1.8013-1.85940.20441370.169725742711100
1.8594-1.92580.1991400.185526232763100
1.9258-2.00290.2261390.171626142753100
2.0029-2.0940.21451400.168126282768100
2.094-2.20430.18951390.163426132752100
2.2043-2.34230.18051370.17926252762100
2.3423-2.5230.18851420.174926602802100
2.523-2.77660.21091400.178326372777100
2.7766-3.17760.21541430.182126772820100
3.1776-4.00050.15751400.15432620276097
4.0005-24.18520.15321480.1562770291898

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