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- PDB-6j7y: Human mitochondrial Oligoribonuclease in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 6j7y
TitleHuman mitochondrial Oligoribonuclease in complex with DNA
Components
  • DNA (5'-D(P*TP*T)-3')
  • Oligoribonuclease, mitochondrial
KeywordsHYDROLASE / Exoribonuclease / Mitochonrial Oligoribonuclease
Function / homology
Function and homology information


Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix ...Mitochondrial RNA degradation / Hydrolases; Acting on ester bonds; Exonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / 3'-5'-DNA exonuclease activity / nucleotide metabolic process / nucleobase-containing compound metabolic process / 3'-5' exonuclease activity / mitochondrial intermembrane space / 3'-5'-RNA exonuclease activity / nucleic acid binding / mitochondrial matrix / focal adhesion / nucleolus / magnesium ion binding / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Oligoribonuclease / Exonuclease / Exonuclease, RNase T/DNA polymerase III / EXOIII / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / Oligoribonuclease, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsChu, L.Y. / Agrawal, S. / Yuan, H.S.
CitationJournal: Rna / Year: 2019
Title: Structural insights into nanoRNA degradation by human Rexo2.
Authors: Chu, L.Y. / Agrawal, S. / Chen, Y.P. / Yang, W.Z. / Yuan, H.S.
History
DepositionJan 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Oligoribonuclease, mitochondrial
A: Oligoribonuclease, mitochondrial
C: DNA (5'-D(P*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4935
Polymers43,4453
Non-polymers492
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-36 kcal/mol
Surface area13880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.282, 125.293, 85.478
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Oligoribonuclease, mitochondrial / RNA exonuclease 2 homolog / Small fragment nuclease


Mass: 21440.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REXO2, SFN, SMFN, CGI-114 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9Y3B8, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(P*TP*T)-3')


Mass: 563.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Ammonium citrate dibasic, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23925 / % possible obs: 99.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.079 / Χ2: 2.446 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.2-2.246.80.56511721.585198.6
2.24-2.286.80.50111551.548199.9
2.28-2.326.80.43311871.633198.7
2.32-2.376.90.37811861.577199
2.37-2.426.80.35611711.642198.9
2.42-2.486.80.30511821.677199.9
2.48-2.546.80.26811881.697199.3
2.54-2.616.80.22411801.644199.2
2.61-2.696.80.19711721.683199.3
2.69-2.776.80.16611881.834199.2
2.77-2.876.80.14811882.098199.5
2.87-2.996.80.13111932.527199.5
2.99-3.126.80.1112012.527199.1
3.12-3.296.80.08511982.371199.7
3.29-3.496.70.06811952.416199.6
3.49-3.766.80.0612073.308199.8
3.76-4.146.70.05912094.28199.8
4.14-4.746.70.05212284.786199.7
4.74-5.976.60.04212333.38199.7
5.97-506.20.02912924.651198.5
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IGI

2igi


Resolution: 2.203→28.34 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2438 1938 8.34 %
Rwork0.1982 --
obs0.2021 23239 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.46 Å2 / Biso mean: 42.5753 Å2 / Biso min: 15.94 Å2
Refinement stepCycle: final / Resolution: 2.203→28.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2507 40 2 116 2665
Biso mean--63.4 47.9 -
Num. residues----306
LS refinement shellResolution: 2.2026→2.2576 Å
RfactorNum. reflection% reflection
Rfree0.3325 119 -
Rwork0.2217 1404 -
obs--91 %
Refinement TLS params.Method: refined / Origin x: 13.327 Å / Origin y: 38.5978 Å / Origin z: 42.4489 Å
111213212223313233
T0.2579 Å2-0.0355 Å2-0.0203 Å2-0.1846 Å2-0.027 Å2--0.1961 Å2
L1.9289 °2-0.3001 °20.2651 °2-0.2146 °2-0.2707 °2--0.8616 °2
S0.0628 Å °-0.0624 Å °-0.103 Å °0.0692 Å °-0.0244 Å °0.0567 Å °0.1476 Å °-0.0522 Å °-0.0203 Å °
Refinement TLS groupSelection details: all

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