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- PDB-6m3u: Crystal structure of the mouse endonuclease EndoG(H138A/C100A), s... -

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Basic information

Entry
Database: PDB / ID: 6m3u
TitleCrystal structure of the mouse endonuclease EndoG(H138A/C100A), space group C2
ComponentsEndonuclease G, mitochondrial
KeywordsAPOPTOSIS / EndoG / DNase
Function / homology
Function and homology information


mitochondrial DNA catabolic process / positive regulation of hydrogen peroxide-mediated programmed cell death / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of mitochondrial DNA replication / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / positive regulation of mitochondrial DNA replication / 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 / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPark, K.H. / Woo, E.J.
CitationJournal: To Be Published
Title: Crystal structure of the mouse endonuclease EndoG(H138A/C100A), space group C2
Authors: Park, K.H. / Woo, E.J.
History
DepositionMar 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)109,8924
Polymers109,8924
Non-polymers00
Water5,152286
1
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial


Theoretical massNumber of molelcules
Total (without water)54,9462
Polymers54,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-32 kcal/mol
Surface area19910 Å2
MethodPISA
2
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial


Theoretical massNumber of molelcules
Total (without water)54,9462
Polymers54,9462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-28 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)252.407, 81.340, 54.684
Angle α, β, γ (deg.)90.000, 102.170, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Endonuclease G, mitochondrial / Endo G


Mass: 27472.879 Da / Num. of mol.: 4 / Mutation: H138A/C110A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 3350, 0.1M HEPES at pH 7.5, 0.18M Ammonium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→42.19 Å / Num. obs: 45823 / % possible obs: 98.1 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.56 Å2 / Rsym value: 0.079 / Net I/σ(I): 16.94
Reflection shellResolution: 2.32→2.37 Å / Num. unique obs: 2429 / Rsym value: 0.43 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M3F

6m3f


Resolution: 2.32→42.19 Å / SU ML: 0.2689 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9872
RfactorNum. reflection% reflection
Rfree0.2375 2297 5.01 %
Rwork0.2014 --
obs0.2032 45823 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.3 Å2
Refinement stepCycle: LAST / Resolution: 2.32→42.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7351 0 0 286 7637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00617527
X-RAY DIFFRACTIONf_angle_d1.15510231
X-RAY DIFFRACTIONf_chiral_restr0.06641099
X-RAY DIFFRACTIONf_plane_restr0.00771357
X-RAY DIFFRACTIONf_dihedral_angle_d40.00291861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.370.30091150.25782429X-RAY DIFFRACTION87.06
2.37-2.430.35151540.25322657X-RAY DIFFRACTION97.5
2.43-2.490.29151310.24642765X-RAY DIFFRACTION97.94
2.49-2.550.31071470.24142670X-RAY DIFFRACTION97.68
2.55-2.630.29381480.23942726X-RAY DIFFRACTION97.79
2.63-2.710.29661360.23932736X-RAY DIFFRACTION98.05
2.71-2.810.23391310.23392720X-RAY DIFFRACTION98.31
2.81-2.920.2761290.23222741X-RAY DIFFRACTION98.25
2.92-3.060.2961440.22982758X-RAY DIFFRACTION98.41
3.06-3.220.24371330.22152747X-RAY DIFFRACTION98.7
3.22-3.420.26821470.21682773X-RAY DIFFRACTION98.58
3.42-3.680.23211500.20292749X-RAY DIFFRACTION98.87
3.68-4.050.21781640.18862722X-RAY DIFFRACTION99.01
4.05-4.640.18861630.15482756X-RAY DIFFRACTION98.68
4.64-5.840.19831530.16762776X-RAY DIFFRACTION98.89
5.84-80.19841520.17962801X-RAY DIFFRACTION97.36
Refinement TLS params.Method: refined / Origin x: 37.3535081809 Å / Origin y: -54.8194027591 Å / Origin z: -26.8500094476 Å
111213212223313233
T0.239976699918 Å20.0124955801371 Å2-0.0053288502711 Å2-0.232972552653 Å20.122429017861 Å2--0.188597211659 Å2
L0.661105747255 °20.00328828469292 °20.00551200633436 °2-0.530017195918 °20.311168574098 °2--0.38578392908 °2
S0.00797103505431 Å °-0.0697164033937 Å °-0.0160369821016 Å °0.0299451392118 Å °0.0307081718912 Å °-0.0363546207439 Å °0.0156034185474 Å °0.0140499538834 Å °-0.0392745164595 Å °
Refinement TLS groupSelection details: all

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