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- PDB-9fxn: Human mitochondrial nuclease EXOG (hEXOG) -

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Basic information

Entry
Database: PDB / ID: 9fxn
TitleHuman mitochondrial nuclease EXOG (hEXOG)
ComponentsNuclease EXOG, mitochondrial
KeywordsHYDROLASE / DNA-repair enzyme / Mitochondrial
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / protein-containing complex / mitochondrion / metal ion binding / nucleus
Similarity search - Function
EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / Non-specific endonuclease / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / His-Me finger superfamily
Similarity search - Domain/homology
Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsKarasinska, J.M. / Szymanski, M.R.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
European Molecular Biology Organization (EMBO)European Union
CitationJournal: Nat Commun / Year: 2017
Title: Human mitochondrial nuclease EXOG (hEXOG)
Authors: Karasinska, J.M. / Szymanski, M.R.
History
DepositionJul 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclease EXOG, mitochondrial
B: Nuclease EXOG, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7334
Polymers72,6842
Non-polymers492
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-47 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.550, 83.560, 74.390
Angle α, β, γ (deg.)90.000, 113.510, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 60 through 62 or resid 64...
d_2ens_1(chain "B" and (resid 60 through 62 or resid 64...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALALEULEUAA60 - 623 - 5
d_12GLNGLNARGARGAA64 - 1097 - 52
d_13HISHISCYSCYSAA111 - 11254 - 55
d_14PHEPHEPHEPHEAA114 - 25857 - 201
d_15PROPROALAALAAA260 - 319203 - 262
d_16SERSERILEILEAA321 - 337264 - 280
d_17PROPROGLUGLUAA339 - 348282 - 291
d_18LYSLYSLEULEUAA350 - 354293 - 297
d_19ALAALAGLUGLUAA356 - 358299 - 301
d_21ALAALALEULEUBB60 - 623 - 5
d_22GLNGLNARGARGBB64 - 1097 - 52
d_23HISHISCYSCYSBB111 - 11254 - 55
d_24PHEPHEPHEPHEBB114 - 25857 - 201
d_25PROPROALAALABB260 - 319203 - 262
d_26SERSERILEILEBB321 - 337264 - 280
d_27PROPROGLUGLUBB339 - 348282 - 291
d_28LYSLYSLEULEUBB350 - 354293 - 297
d_29ALAALAGLUGLUBB356 - 358299 - 301

NCS oper: (Code: givenMatrix: (-0.995103399004, -0.098654216937, -0.00604737714947), (-0.0988361278685, 0.992709094548, 0.0689932853959), (-0.0008031922502, 0.0692531521471, -0.997598795007)Vector: - ...NCS oper: (Code: given
Matrix: (-0.995103399004, -0.098654216937, -0.00604737714947), (-0.0988361278685, 0.992709094548, 0.0689932853959), (-0.0008031922502, 0.0692531521471, -0.997598795007)
Vector: -28.0603618594, 0.615656780684, -64.6588512709)

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Components

#1: Protein Nuclease EXOG, mitochondrial / Endonuclease G-like 1 / Endo G-like 1


Mass: 36342.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 16.5 % PEG 8000, 0.1 M Tris-HCL, 0.3 M magnesium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03326 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03326 Å / Relative weight: 1
ReflectionResolution: 1.62→40.55 Å / Num. obs: 97632 / % possible obs: 93 % / Redundancy: 6.64 % / Biso Wilson estimate: 34.17 Å2 / CC1/2: 0.99 / Net I/σ(I): 1.01
Reflection shellResolution: 1.62→1.72 Å / Mean I/σ(I) obs: 1.01 / Num. unique obs: 97632 / CC1/2: 0.99 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→40.55 Å / SU ML: 0.2302 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.5008
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.228 2100 2.15 %
Rwork0.1571 95468 -
obs0.1587 97568 93.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.08 Å2
Refinement stepCycle: LAST / Resolution: 1.62→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4835 0 2 252 5089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00534949
X-RAY DIFFRACTIONf_angle_d0.84196693
X-RAY DIFFRACTIONf_chiral_restr0.0453719
X-RAY DIFFRACTIONf_plane_restr0.0148873
X-RAY DIFFRACTIONf_dihedral_angle_d5.3364655
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.774025205039 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.4175890.39194074X-RAY DIFFRACTION59.78
1.66-1.70.41030.34144674X-RAY DIFFRACTION68.91
1.7-1.740.35231220.29135541X-RAY DIFFRACTION80.95
1.74-1.80.29861430.25816506X-RAY DIFFRACTION95.75
1.8-1.850.29231500.22966798X-RAY DIFFRACTION99.76
1.85-1.920.28021500.19046804X-RAY DIFFRACTION99.64
1.92-20.2281490.15446797X-RAY DIFFRACTION99.68
2-2.090.21431490.14946780X-RAY DIFFRACTION99.54
2.09-2.20.2481480.15196719X-RAY DIFFRACTION97.99
2.2-2.340.20641470.15346678X-RAY DIFFRACTION98.12
2.34-2.520.21971490.15936791X-RAY DIFFRACTION99.71
2.52-2.770.2651510.17026844X-RAY DIFFRACTION99.56
2.77-3.170.24391470.16756704X-RAY DIFFRACTION97.87
3.17-3.990.19821510.14586870X-RAY DIFFRACTION99.66
3.99-40.550.21671520.13586888X-RAY DIFFRACTION98.82

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