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- PDB-6wre: Crystal structure of mouse DXO in complex with 5'-OH RNA substrat... -

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Basic information

Entry
Database: PDB / ID: 6wre
TitleCrystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion
Components
  • Decapping and exoribonuclease protein
  • RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')
KeywordsHYDROLASE / 5'-OH / RNA / cap
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / 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 / RNA destabilization / mRNA 5'-diphosphatase activity / 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 / nucleus / cytosol
Similarity search - Function
RAI1-like / RAI1 like PD-(D/E)XK nuclease / RAI1-like family
Similarity search - Domain/homology
3'-URIDINEMONOPHOSPHATE / RNA / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDoamekpor, S.K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118093 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: A novel 5'-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes.
Authors: Doamekpor, S.K. / Gozdek, A. / Kwasnik, A. / Kufel, J. / Tong, L.
History
DepositionApr 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.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
D: RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3214
Polymers44,9572
Non-polymers3642
Water2,306128
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)50.182, 87.795, 53.880
Angle α, β, γ (deg.)90.000, 112.350, 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 / 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: RNA chain RNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')


Mass: 1824.169 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-OH / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-U3P / 3'-URIDINEMONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→49.83 Å / Num. obs: 29081 / % possible obs: 96 % / Redundancy: 1.99 % / Biso Wilson estimate: 42.125 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.072 / Χ2: 1.108 / Net I/σ(I): 8.91 / Num. measured all: 110559 / Scaling rejects: 10
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
2-2.051.9530.6391.917548423938640.6630.85691.2
2.05-2.111.9020.4872.37613420940030.7910.65295.1
2.11-2.171.8170.3552.986966400338340.8610.47895.8
2.17-2.232.0320.313.597953399339140.9070.41698
2.23-2.312.0630.2564.257655378437100.9330.34398
2.31-2.392.0670.2264.877566371736600.9470.30298.5
2.39-2.482.0550.1985.477082351834470.9530.26598
2.48-2.582.0360.1436.566895346333860.9740.19297.8
2.58-2.692.0040.137.036456330232210.9780.17497.5
2.69-2.821.9910.0928.916028312330270.9870.12496.9
2.82-2.981.9170.07410.195476300728560.990.195
2.98-3.161.8070.05511.734878284627000.9930.07494.9
3.16-3.382.0950.04614.815367265925620.9950.06296.4
3.38-3.652.0910.0417.414894245923410.9950.05495.2
3.65-3.992.0630.03519.644391224621280.9960.04894.7
3.99-4.472.0420.03420.744077210619970.9960.04694.8
4.47-5.161.9760.02921.243365180117030.9970.03994.6
5.16-6.321.820.03119.82583155014190.9960.04291.5
6.32-8.932.1320.02922.512428117811390.9970.03896.7
8.93-49.832.0840.02324.7513386616420.9980.03197.1

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Processing

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

4j7l


Resolution: 2→49.83 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.06
RfactorNum. reflection% reflection
Rfree0.22 1999 6.88 %
Rwork0.1874 --
obs0.1896 29060 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.56 Å2 / Biso mean: 42.1002 Å2 / Biso min: 23.3 Å2
Refinement stepCycle: final / Resolution: 2→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 81 22 128 3120
Biso mean--75.53 45.33 -
Num. residues----363
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 (%)
2-2.050.42941400.33991830197095
2.05-2.10.35631270.31221959208699
2.1-2.160.29911520.26861898205099
2.16-2.230.27761530.246119382091100
2.23-2.310.27471400.21419332073100
2.31-2.410.23051300.217319582088100
2.41-2.520.25271520.196719452097100
2.52-2.650.3021410.215519312072100
2.65-2.810.23041470.200119292076100
2.82-3.030.22641370.19321949208699
3.03-3.340.2181490.19731916206599
3.34-3.820.18141410.15961946208799
3.82-4.810.15541420.14311956209899
4.81-49.830.20871480.16651973212199

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