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- PDB-6lyf: Crystal structure of the mouse endonuclease EndoG(H138A/Se-Met) -

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Basic information

Entry
Database: PDB / ID: 6lyf
TitleCrystal structure of the mouse endonuclease EndoG(H138A/Se-Met)
ComponentsEndonuclease G, mitochondrial
KeywordsAPOPTOSIS / EndoG / DNase / mitochondria
Function / homology
Function and homology information


mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / DNA catabolic process / negative regulation of TOR signaling / response to tumor necrosis factor / response to mechanical stimulus ...mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / positive regulation of mitochondrial DNA replication / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of apoptotic DNA fragmentation / apoptotic DNA fragmentation / DNA catabolic process / negative regulation of TOR signaling / response to tumor necrosis factor / response to mechanical stimulus / positive regulation of autophagy / cellular response to calcium ion / DNA endonuclease activity / cellular response to glucose stimulus / response to estradiol / cellular response to oxidative stress / perikaryon / cellular response to hypoxia / in utero embryonic development / nucleic acid binding / positive regulation of apoptotic process / response to antibiotic / DNA damage response / perinuclear region of cytoplasm / magnesium ion binding / protein homodimerization activity / mitochondrion
Similarity search - Function
DNA/RNA non-specific endonuclease, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 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, active site / DNA/RNA non-specific endonucleases active site. / Non-specific endonuclease / Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsPark, K.H. / Woo, E.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the mouse endonuclease G.
Authors: Park, K.H. / Yoon, S.M. / Song, H.N. / Yang, J.H. / Ryu, S.E. / Woo, E.J.
History
DepositionFeb 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4928
Polymers110,3954
Non-polymers974
Water3,243180
1
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2464
Polymers55,1972
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-43 kcal/mol
Surface area19060 Å2
MethodPISA
2
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2464
Polymers55,1972
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-45 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.200, 81.880, 88.657
Angle α, β, γ (deg.)90.000, 97.590, 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-ID
11
21
31
41

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Components

#1: Protein
Endonuclease G, mitochondrial / Endo G


Mass: 27598.734 Da / Num. of mol.: 4 / Mutation: H138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endog / Production host: Escherichia coli (E. coli)
References: UniProt: O08600, 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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200mM NaCl, 1mM CdCl2, 100mM CHES, 10mM CTAB, 5% glycerol, 5% MPD

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→48.12 Å / Num. obs: 56219 / % possible obs: 99.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 39.44 Å2 / Rsym value: 0.086 / Net I/σ(I): 13.5
Reflection shellResolution: 2.8→2.85 Å / Num. unique obs: 28825 / Rsym value: 0.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→48.12 Å / SU ML: 0.3627 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.2075
RfactorNum. reflection% reflection
Rfree0.2569 2448 4.95 %
Rwork0.1986 --
obs0.2015 49489 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.19 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 3 180 7194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00647186
X-RAY DIFFRACTIONf_angle_d1.06529771
X-RAY DIFFRACTIONf_chiral_restr0.05551037
X-RAY DIFFRACTIONf_plane_restr0.00561300
X-RAY DIFFRACTIONf_dihedral_angle_d6.89264295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.860.37481480.26362749X-RAY DIFFRACTION99.69
2.86-2.920.31741270.25132750X-RAY DIFFRACTION99.9
2.92-2.990.31431290.24662799X-RAY DIFFRACTION99.93
2.99-3.060.29121330.24712776X-RAY DIFFRACTION99.93
3.06-3.140.27451640.23212784X-RAY DIFFRACTION100
3.14-3.240.2981180.23492754X-RAY DIFFRACTION99.97
3.24-3.340.32141500.21392748X-RAY DIFFRACTION100
3.34-3.460.26161780.20782782X-RAY DIFFRACTION99.97
3.46-3.60.27911700.20282696X-RAY DIFFRACTION99.97
3.6-3.760.27051540.19222808X-RAY DIFFRACTION100
3.76-3.960.28051080.19272799X-RAY DIFFRACTION99.97
3.96-4.210.22581590.17392735X-RAY DIFFRACTION100
4.21-4.530.20881330.15872809X-RAY DIFFRACTION100
4.53-4.990.25051230.16232783X-RAY DIFFRACTION99.93
4.99-5.710.22451590.17922746X-RAY DIFFRACTION99.97
5.71-7.190.23441510.20552780X-RAY DIFFRACTION99.9
7.19-48.120.19881440.19382743X-RAY DIFFRACTION99.35
Refinement TLS params.Method: refined / Origin x: 10.3241861153 Å / Origin y: 27.5101005381 Å / Origin z: 67.3070337233 Å
111213212223313233
T0.183892301141 Å20.0294381307183 Å20.0111175278395 Å2-0.254263626312 Å2-0.0380992317317 Å2--0.19423422137 Å2
L1.02074254633 °2-1.09571805466 °20.421320423789 °2-1.65995303719 °2-0.6397004096 °2--0.362517634919 °2
S-0.0191676305243 Å °-0.109720461529 Å °0.155120163653 Å °-0.0747571606314 Å °0.0638795536379 Å °-0.0851151978535 Å °-0.00746507520282 Å °-0.125770794218 Å °-0.0420742442041 Å °
Refinement TLS groupSelection details: all

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