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- PDB-6wuf: Crystal structure of mouse DXO in complex with 3'-FADP -

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Basic information

Entry
Database: PDB / ID: 6wuf
TitleCrystal structure of mouse DXO in complex with 3'-FADP
ComponentsDecapping and exoribonuclease protein
KeywordsHYDROLASE / FAD / 3'-FADP / RNA / cap / decapping
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / mRNA 5'-diphosphatase activity / RNA destabilization / NAD-cap decapping / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides ...RNA NAD+-cap (NAD+-forming) hydrolase activity / mRNA 5'-diphosphatase activity / RNA destabilization / NAD-cap decapping / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / nuclear-transcribed mRNA catabolic process / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / mRNA binding / magnesium ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family
Similarity search - Domain/homology
Chem-UBG / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsDoamekpor, S.K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)R35GM118093 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: DXO/Rai1 enzymes remove 5'-end FAD and dephospho-CoA caps on RNAs.
Authors: Doamekpor, S.K. / Grudzien-Nogalska, E. / Mlynarska-Cieslak, A. / Kowalska, J. / Kiledjian, M. / Tong, L.
History
DepositionMay 4, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decapping and exoribonuclease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3913
Polymers47,4641
Non-polymers9282
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.956, 87.877, 53.289
Angle α, β, γ (deg.)90.000, 113.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Decapping and exoribonuclease protein / DXO / Dom-3 homolog Z


Mass: 47463.625 Da / Num. of mol.: 1 / Mutation: E192S/E234Q/E253Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dxo, Dom3z, Ng6 / Production host: Escherichia coli (E. coli)
References: UniProt: O70348, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-UBG / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)


Mass: 865.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H34N9O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 23% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→48.89 Å / Num. obs: 54771 / % possible obs: 94.9 % / Redundancy: 2.351 % / Biso Wilson estimate: 25.785 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.096 / Χ2: 1.056 / Net I/σ(I): 10.6 / Num. measured all: 244274
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.642.2340.4761.916747802574960.8230.61293.4
1.64-1.692.3620.4032.2718019796776300.8760.51895.8
1.69-1.742.3130.342.716730762772330.90.43894.8
1.74-1.792.1350.2513.514819751269400.9370.32692.4
1.79-1.852.3250.2174.4915814722468020.9530.2894.2
1.85-1.912.4110.185.5815927697566060.9690.23194.7
1.91-1.992.3650.1516.814980672863340.9720.19494.1
1.99-2.072.3210.1258.4914114648460820.9760.16193.8
2.07-2.162.320.12610.1913717625059120.9730.16294.6
2.16-2.272.2970.12311.5412906595256190.9620.15794.4
2.27-2.392.2570.113.3412122568153720.9780.12894.6
2.39-2.532.10.0914.4310254533048830.9740.11791.6
2.53-2.712.4280.08816.6911670498348070.9820.11296.5
2.71-2.932.6080.09319.512149473646590.9840.11598.4
2.93-3.22.6160.08121.0311124431242520.9880.09998.6
3.2-3.582.580.06123.519849389938180.9930.07597.9
3.58-4.142.5120.04625.478466343133700.9950.05798.2
4.14-5.072.2820.03925.576243289627360.9960.0594.5
5.07-7.172.620.03926.565835225822270.9960.04898.6
7.17-48.892.4880.03527.912789122411210.9960.04591.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J7L

4j7l


Resolution: 1.6→48.89 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2338 2001 3.66 %
Rwork0.1998 52742 -
obs0.2011 54743 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.51 Å2 / Biso mean: 25.8897 Å2 / Biso min: 10.9 Å2
Refinement stepCycle: final / Resolution: 1.6→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 67 372 3325
Biso mean--33.17 38.53 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063079
X-RAY DIFFRACTIONf_angle_d0.8984214
X-RAY DIFFRACTIONf_dihedral_angle_d18.972427
X-RAY DIFFRACTIONf_chiral_restr0.053419
X-RAY DIFFRACTIONf_plane_restr0.007551
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6-1.640.29411350.2766365197
1.64-1.690.31191420.2726379499
1.69-1.740.33931440.2744372599
1.74-1.790.27851430.2725374398
1.79-1.860.2851470.2533373599
1.86-1.930.27431400.2616377599
1.93-2.020.25711370.2571377399
2.02-2.120.26491380.2464375999
2.12-2.260.30631470.232379299
2.26-2.430.24311510.1976376199
2.43-2.680.24541420.193377699
2.68-3.060.23231460.17533810100
3.06-3.860.1831490.15683823100
3.86-48.890.17561400.1609382598

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