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- PDB-6dkn: CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DECAPPING NUCLEASE DXO1 -

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Basic information

Entry
Database: PDB / ID: 6dkn
TitleCRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA DECAPPING NUCLEASE DXO1
ComponentsDecapping nuclease DXO homolog, chloroplastic
KeywordsHYDROLASE / Decapping / Nuclease
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / 5'-3' RNA exonuclease activity / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / 3'-5'-RNA exonuclease activity / hydrolase activity / nucleotide binding / RNA binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
NAD-capped RNA hydrolase DXO1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTong, L. / Wang, V.Y.F.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35GM118093 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
Citation
Journal: Nucleic Acids Res. / Year: 2019
Title: Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity.
Authors: Kwasnik, A. / Wang, V.Y. / Krzyszton, M. / Gozdek, A. / Zakrzewska-Placzek, M. / Stepniak, K. / Poznanski, J. / Tong, L. / Kufel, J.
#1: Journal: Nucleic Acids Res. / Year: 2019
Title: Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity.
Authors: Kwasnik, A. / Wang, V.Y. / Krzyszton, M. / Gozdek, A. / Zakrzewska-Placzek, M. / Stepniak, K. / Poznanski, J. / Tong, L. / Kufel, J.
History
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Decapping nuclease DXO homolog, chloroplastic
B: Decapping nuclease DXO homolog, chloroplastic


Theoretical massNumber of molelcules
Total (without water)80,6512
Polymers80,6512
Non-polymers00
Water8,413467
1
A: Decapping nuclease DXO homolog, chloroplastic


Theoretical massNumber of molelcules
Total (without water)40,3261
Polymers40,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Decapping nuclease DXO homolog, chloroplastic


Theoretical massNumber of molelcules
Total (without water)40,3261
Polymers40,3261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.080, 80.878, 125.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 310 - 312 / Label seq-ID: 115 - 117

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.963374, -0.180709, -0.198129), (0.2303, -0.936043, -0.266054), (-0.137379, -0.301939, 0.943377)126.07611, 139.90512, 40.01269

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Components

#1: Protein Decapping nuclease DXO homolog, chloroplastic


Mass: 40325.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g17620, dl4845w, FCAALL.74 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RY73, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NH4F and 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 61925 / % possible obs: 98.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.7
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.4 / Num. unique obs: 8773

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FQG

3fqg


Resolution: 1.8→48.52 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.896 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24202 3312 5.1 %RANDOM
Rwork0.20081 ---
obs0.20291 61925 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å20 Å2
2---0.67 Å2-0 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 0 0 467 5943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195592
X-RAY DIFFRACTIONr_bond_other_d0.0010.025277
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9467537
X-RAY DIFFRACTIONr_angle_other_deg0.751312092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635669
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38223.11299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5315990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6591556
X-RAY DIFFRACTIONr_chiral_restr0.0810.2798
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026364
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021400
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 57 / Type: tight thermal / Rms dev position: 5.35 Å / Weight position: 0.5
LS refinement shellResolution: 1.8→1.897 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.301 483 -
Rwork0.254 8773 -
obs--97.47 %

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