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- PDB-6aiy: Crystal structure of DXO (E234A mutant) in complex with adenosine... -

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Basic information

Entry
Database: PDB / ID: 6aiy
TitleCrystal structure of DXO (E234A mutant) in complex with adenosine 3', 5' bisphosphate and two magnesium ions
ComponentsDecapping and exoribonuclease protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 5'to 3' exoribonuclease / DXO / adenosine 3' / 5' bisphosphate / nuclease inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
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
ADENOSINE-3'-5'-DIPHOSPHATE / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.902 Å
AuthorsChang, J.H. / Tong, L.
Funding support Korea, Republic Of, United States, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)2016R1C1B2009691 Korea, Republic Of
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118093 United States
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Molecular mechanism for the inhibition of DXO by adenosine 3',5'-bisphosphate.
Authors: Yun, J.S. / Yoon, J.H. / Choi, Y.J. / Son, Y.J. / Kim, S. / Tong, L. / Chang, J.H.
History
DepositionAug 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)43,5504
Polymers43,0741
Non-polymers4763
Water4,720262
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-26 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.499, 88.081, 50.040
Angle α, β, γ (deg.)90.00, 114.42, 90.00
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: 43074.496 Da / Num. of mol.: 1 / Mutation: E234A
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-A3P / ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 2.17 Å3/Da / Density % sol: 43.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 100mM pAp, 10mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 28870 / % possible obs: 99 % / Redundancy: 3.8 % / Net I/σ(I): 21.7
Reflection shellResolution: 1.9→1.97 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 1.902→40.469 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2004 7.02 %
Rwork0.1702 --
obs0.1725 28537 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→40.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2885 0 29 262 3176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063023
X-RAY DIFFRACTIONf_angle_d0.8574130
X-RAY DIFFRACTIONf_dihedral_angle_d5.5952476
X-RAY DIFFRACTIONf_chiral_restr0.052414
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9016-1.94920.29031320.211851X-RAY DIFFRACTION96
1.9492-2.00180.25981480.20021862X-RAY DIFFRACTION98
2.0018-2.06080.23161340.18871847X-RAY DIFFRACTION99
2.0608-2.12730.23361450.1781902X-RAY DIFFRACTION99
2.1273-2.20330.20271400.16941909X-RAY DIFFRACTION99
2.2033-2.29150.18791450.17731866X-RAY DIFFRACTION99
2.2915-2.39580.2231340.17241908X-RAY DIFFRACTION99
2.3958-2.52210.22171480.1791883X-RAY DIFFRACTION99
2.5221-2.68010.20581480.18711901X-RAY DIFFRACTION99
2.6801-2.88690.22421500.18191905X-RAY DIFFRACTION100
2.8869-3.17740.23461370.17661907X-RAY DIFFRACTION100
3.1774-3.63690.19881480.16291939X-RAY DIFFRACTION100
3.6369-4.58110.16181490.14181929X-RAY DIFFRACTION100
4.5811-40.47860.18391460.171924X-RAY DIFFRACTION98

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