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- PDB-5uli: Crystal Structure of mouse DXO in complex with (3'-NADP)+ and cal... -

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Basic information

Entry
Database: PDB / ID: 5uli
TitleCrystal Structure of mouse DXO in complex with (3'-NADP)+ and calcium ion
ComponentsDecapping and exoribonuclease protein
KeywordsHYDROLASE / NADP
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-0WD / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDoamekpor, S.K. / Tong, L.
CitationJournal: Cell / Year: 2017
Title: 5' End Nicotinamide Adenine Dinucleotide Cap in Human Cells Promotes RNA Decay through DXO-Mediated deNADding.
Authors: Jiao, X. / Doamekpor, S.K. / Bird, J.G. / Nickels, B.E. / Tong, L. / Hart, R.P. / Kiledjian, M.
History
DepositionJan 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decapping and exoribonuclease protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9183
Polymers43,1331
Non-polymers7852
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.867, 87.678, 53.158
Angle α, β, γ (deg.)90.000, 113.020, 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: 43132.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dxo, Dom3z, Ng6 / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta
References: UniProt: O70348, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-0WD / [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.61 Å3/Da / Density % sol: 52.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→48.926 Å / Num. obs: 47716 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 2.902 % / Biso Wilson estimate: 26.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.088 / Χ2: 0.943 / Net I/σ(I): 12.06 / Num. measured all: 137567
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
2.1-2.232.8410.3962.8121633780976150.8420.48897.5
2.23-2.382.9010.2833.9920917733972100.9060.34998.2
2.38-2.582.7810.2025.5118519679866590.9390.25198
2.58-2.823.0020.1378.2118583627461910.9720.16898.7
2.82-3.152.9230.08612.216483572356400.9870.10698.5
3.15-3.642.9140.05119.2414269496148960.9950.06398.7
3.64-4.452.9650.03427.7412449427341980.9980.04298.2
4.45-6.262.9250.03129.389386328732090.9980.03897.6
6.26-48.9262.9720.02533.685326183117920.9990.0397.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.13 Å48.93 Å
Translation6.13 Å48.93 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.926 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 3673 7.7 %
Rwork0.1613 44043 -
obs0.1649 47716 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.64 Å2 / Biso mean: 30.9009 Å2 / Biso min: 13.7 Å2
Refinement stepCycle: final / Resolution: 2.1→48.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 74 151 3114
Biso mean--56.36 34.85 -
Num. residues----358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133100
X-RAY DIFFRACTIONf_angle_d1.3564245
X-RAY DIFFRACTIONf_chiral_restr0.056423
X-RAY DIFFRACTIONf_plane_restr0.008561
X-RAY DIFFRACTIONf_dihedral_angle_d13.311142
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.26473680.23134409477799
2.1751-2.26210.25453510.20754416476799
2.2621-2.36510.22883670.1964427479498
2.3651-2.48980.23053740.17844355472998
2.4898-2.64580.23443750.17244389476499
2.6458-2.850.22673640.16854410477499
2.85-3.13680.22133750.16324450482599
3.1368-3.59060.19583670.15484394476199
3.5906-4.52330.1763620.13394397475999
4.5233-48.93970.1843700.1444396476698

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