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- PDB-6wui: Crystal Structure of mutant S. pombe Rai1 (E150S/E199Q/E239Q) in ... -

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Basic information

Entry
Database: PDB / ID: 6wui
TitleCrystal Structure of mutant S. pombe Rai1 (E150S/E199Q/E239Q) in complex with 3'-FADP
ComponentsDecapping nuclease din1
KeywordsHYDROLASE / FAD / 3'-FADP / RNA / cap / decapping / Rai1
Function / homology
Function and homology information


5'-hydroxyl dinucleotide hydrolase / Las1 complex / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / RNA NAD-cap (NAD-forming) hydrolase activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid phosphodiester bond hydrolysis / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / GDP binding ...5'-hydroxyl dinucleotide hydrolase / Las1 complex / nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' / RNA NAD-cap (NAD-forming) hydrolase activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid phosphodiester bond hydrolysis / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / GDP binding / mRNA processing / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RAI1 like PD-(D/E)XK nuclease / RAI1-like / RAI1-like family
Similarity search - Domain/homology
Chem-UBG / Decapping nuclease din1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decapping nuclease din1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7932
Polymers42,9271
Non-polymers8661
Water2,504139
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)101.292, 60.428, 72.788
Angle α, β, γ (deg.)90.000, 104.120, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

#1: Protein Decapping nuclease din1 / Dhp1-interacting protein 1


Mass: 42927.004 Da / Num. of mol.: 1 / Mutation: E150S/E199Q/E239Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: din1, SPAC19D5.06c / Production host: Escherichia coli (E. coli)
References: UniProt: O13836, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% (w/v) PEG 3350, 0.2M MgCl2

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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: 1.9→51.47 Å / Num. obs: 33344 / % possible obs: 97 % / Redundancy: 2.085 % / Biso Wilson estimate: 47.979 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.041 / Χ2: 1.11 / Net I/σ(I): 13.17 / Num. measured all: 132994 / Scaling rejects: 3
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
1.9-1.952.1350.6451.4710020486346940.5450.86896.5
1.95-2.012.1140.4642.029771469546220.7090.62598.4
2.01-2.062.1110.3232.849652463045730.8270.43598.8
2.06-2.132.0970.2443.759222448143970.8980.3398.1
2.13-2.22.0770.1814.838970439443180.9410.24498.3
2.2-2.272.0690.1386.28477420440970.9670.18597.5
2.27-2.362.0390.1037.848035406839400.9780.13996.9
2.36-2.461.9670.0789.567324387337230.9880.10596.1
2.46-2.571.8920.0611.536514371034430.9920.07992.8
2.57-2.692.1560.05114.517610359535290.9940.06898.2
2.69-2.842.180.04117.477205336233050.9960.05598.3
2.84-3.012.1790.03520.866919323331760.9960.04798.2
3.01-3.222.1420.03123.716367303429730.9970.04198
3.22-3.472.1080.02827.065668281226890.9970.03895.6
3.47-3.82.1010.02529.475148257724500.9970.03395.1
3.8-4.252.0350.02430.564520233322210.9980.03295.2
4.25-4.911.8110.02430.153504207719350.9980.03193.2
4.91-6.022.1820.02133.263683174716880.9980.02796.6
6.02-8.512.1770.01933.72859134613130.9990.02697.5
8.51-51.472.1370.01834.6115267307140.9980.02397.8

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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: 3FQG
Resolution: 1.9→51.47 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2095 1999 6 %
Rwork0.1722 31337 -
obs0.1744 33336 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.46 Å2 / Biso mean: 52.9432 Å2 / Biso min: 28.43 Å2
Refinement stepCycle: final / Resolution: 1.9→51.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 57 139 2771
Biso mean--49.08 55.48 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012718
X-RAY DIFFRACTIONf_angle_d1.3293703
X-RAY DIFFRACTIONf_dihedral_angle_d15.095356
X-RAY DIFFRACTIONf_chiral_restr0.061397
X-RAY DIFFRACTIONf_plane_restr0.008457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.950.26881390.26842191233098
1.95-20.27891420.242222262368100
2-2.060.25721440.225422462390100
2.06-2.130.27261430.2222352378100
2.13-2.20.23231440.222602404100
2.2-2.290.24281410.20132217235899
2.29-2.40.24261420.20082234237699
2.4-2.520.25591410.19792206234798
2.52-2.680.21371430.19862245238899
2.68-2.890.22361440.198422472391100
2.89-3.180.22391430.197522532396100
3.18-3.640.18531450.17562259240499
3.64-4.580.20111420.13512233237598
4.59-51.470.1811460.14362285243198

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