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- PDB-6nju: Mouse endonuclease G mutant H97A bound to A-DNA -

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Basic information

Entry
Database: PDB / ID: 6nju
TitleMouse endonuclease G mutant H97A bound to A-DNA
Components
  • DNA (5'-D(CCGGCGCCGG)-3')
  • Endonuclease G, mitochondrial
KeywordsRECOMBINATION / Complex / 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 / cellular response to hypoxia / perikaryon / 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
DNA / Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 1.1Jan 15, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Mar 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 1.4Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Oct 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 1.6Oct 9, 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
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97414
Polymers114,6135
Non-polymers3619
Water4,360242
1
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules

C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
E: DNA (5'-D(CCGGCGCCGG)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,21418
Polymers117,6606
Non-polymers55412
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
2
A: Endonuclease G, mitochondrial
B: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8675
Polymers55,7832
Non-polymers843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-56 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.983, 107.983, 357.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein / DNA chain , 2 types, 5 molecules ABCDE

#1: Protein
Endonuclease G, mitochondrial / Endo G


Mass: 27891.410 Da / Num. of mol.: 4 / Fragment: residues 43-294 / Mutation: H97A
Source method: isolated from a genetically manipulated source
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: DNA chain DNA (5'-D(CCGGCGCCGG)-3')


Mass: 3046.980 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)

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Non-polymers , 4 types, 251 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 22% PEG 1000

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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: Jul 22, 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: 2.35→59.57 Å / Num. obs: 52587 / % possible obs: 99.9 % / Redundancy: 20.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.814 / Rpim(I) all: 0.256 / Net I/σ(I): 5.1
Reflection shellResolution: 2.35→2.42 Å / Redundancy: 19.5 % / Rmerge(I) obs: 6.791 / Num. unique obs: 4441 / CC1/2: 0.343 / Rpim(I) all: 2.231 / % 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: 2.35→53.992 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.85
RfactorNum. reflection% reflection
Rfree0.2915 2533 4.83 %
Rwork0.2223 --
obs0.2256 52389 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.43 Å2 / Biso mean: 35.7824 Å2 / Biso min: 10.48 Å2
Refinement stepCycle: final / Resolution: 2.35→53.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7213 202 16 243 7674
Biso mean--38.87 32.03 -
Num. residues----914
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.39520.42311360.36462697283399
2.3952-2.44410.37251520.343226732825100
2.4441-2.49730.37331570.314126802837100
2.4973-2.55540.36591360.296727272863100
2.5554-2.61930.3491360.288927212857100
2.6193-2.69010.36531280.285927402868100
2.6901-2.76930.35081340.268427382872100
2.7693-2.85860.33571330.250527322865100
2.8586-2.96080.30741460.248527132859100
2.9608-3.07930.35231330.245827642897100
3.0793-3.21950.27461400.222427422882100
3.2195-3.38920.27711440.211727732917100
3.3892-3.60150.28251300.194727912921100
3.6015-3.87950.28241300.188327782908100
3.8795-4.26970.26541270.175328172944100
4.2697-4.88720.2271610.164328152976100
4.8872-6.1560.24871570.190528593016100
6.156-54.00570.23711530.205530963249100

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