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- PDB-6njt: Mouse endonuclease G mutant - H97A -

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Basic information

Entry
Database: PDB / ID: 6njt
TitleMouse endonuclease G mutant - H97A
ComponentsEndonuclease G, mitochondrial
KeywordsRECOMBINATION / Endonuclease
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
ISOPROPYL ALCOHOL / Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsVander Zanden, C.M. / Ho, E.N. / Czarny, R.S. / Robertson, A.B. / Ho, P.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1515521 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function.
Authors: Vander Zanden, C.M. / Czarny, R.S. / Ho, E.N. / Robertson, A.B. / Ho, P.S.
History
DepositionJan 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,70223
Polymers55,7832
Non-polymers91921
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-101 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.609, 109.609, 118.062
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21B-571-

HOH

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Components

#1: Protein Endonuclease G, mitochondrial / Endo G


Mass: 27891.410 Da / Num. of mol.: 2 / Fragment: residues 43-294 / Mutation: H97A
Source method: isolated from a genetically manipulated source
Details: residues 43-294 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endog / Plasmid: pMal-c2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
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: 3.99 Å3/Da / Density % sol: 69.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 25% isopropanol, 0.2 M MgCl2, 0.1 M HEPES pH 7.6, 0.75 mM G(5HMC) dinucleotide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 17, 2017
RadiationMonochromator: ROSENBAUM-ROCK SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.07→54.8 Å / Num. obs: 50410 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.277 / Rpim(I) all: 0.145 / Net I/σ(I): 8.2
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 7.1 % / Rmerge(I) obs: 2.691 / Num. unique obs: 3865 / CC1/2: 0.319 / Rpim(I) all: 1.618 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
XDSdata reduction
PHASERv2.7.16phasing
Cootv0.8.9.1model building
Aimlessv0.7.1data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKP

5gkp


Resolution: 2.07→49.71 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.4
RfactorNum. reflection% reflection
Rfree0.2134 2543 5.05 %
Rwork0.1839 --
obs0.1854 50343 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.54 Å2 / Biso mean: 32.6545 Å2 / Biso min: 12.54 Å2
Refinement stepCycle: final / Resolution: 2.07→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 45 445 4082
Biso mean--45.28 37.26 -
Num. residues----451
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.07-2.10980.3481560.309726082764
2.1098-2.15290.32761350.28826062741
2.1529-2.19970.25381100.267826542764
2.1997-2.25090.32761430.285525972740
2.2509-2.30720.30841410.256726472788
2.3072-2.36960.24421180.228626722790
2.3696-2.43930.26391120.220826642776
2.4393-2.5180.27031230.221226362759
2.518-2.6080.26321460.202726322778
2.608-2.71240.25681400.203226412781
2.7124-2.83590.23031710.186526172788
2.8359-2.98540.22471130.182726852798
2.9854-3.17240.1981560.184526242780
3.1724-3.41730.23691800.15926432823
3.4173-3.7610.15971290.149226772806
3.761-4.3050.15391800.133526512831
4.305-5.42280.15581550.123927142869
5.4228-49.72410.17731350.179628322967

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