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- PDB-7r6t: Human EXOG complexed with dRP-containing DNA -

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Basic information

Entry
Database: PDB / ID: 7r6t
TitleHuman EXOG complexed with dRP-containing DNA
Components
  • DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
  • DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
  • Nuclease EXOG, mitochondrial
KeywordsDNA BINDING PROTEIN/DNA / Mitochondrial BER / endo/exonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
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; 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 ...EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / 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 / DNA (> 10) / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSzymanski, M.R. / Yin, Y.W.
CitationJournal: To Be Published
Title: Human EXOG possesses strong AP hydrolysis activity
Authors: Szymanski, M.R. / Yin, Y.W.
History
DepositionJun 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
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
D: Nuclease EXOG, mitochondrial
F: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
A: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
C: Nuclease EXOG, mitochondrial
E: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
B: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
L: Nuclease EXOG, mitochondrial
M: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
K: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,21814
Polymers125,0989
Non-polymers1205
Water19811
1
D: Nuclease EXOG, mitochondrial
F: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
A: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7485
Polymers41,6993
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Nuclease EXOG, mitochondrial
E: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
B: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7475
Polymers41,6993
Non-polymers472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: Nuclease EXOG, mitochondrial
M: DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
K: DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7244
Polymers41,6993
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.252, 100.056, 174.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 3 molecules DCL

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


Mass: 35444.203 Da / Num. of mol.: 3 / Mutation: H140A
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

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DNA chain , 2 types, 6 molecules FEMABK

#2: DNA chain DNA (5'-D(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')


Mass: 2911.894 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The mismatch is due to a deoxyribose site. / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')


Mass: 3343.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 16 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28% PEG 4K, 0.2 M Ammonium Acetate, 0.1 M Na Citrate tribasic dihydrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 1, 2021
RadiationMonochromator: Zr filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 26817 / % possible obs: 99 % / Redundancy: 6.4 % / CC1/2: 0.75 / Net I/σ(I): 2.7
Reflection shellResolution: 2.9→3.5 Å / Redundancy: 6.3 % / Num. unique obs: 2612 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.17refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T5C

5t5c


Resolution: 2.9→37.97 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.286 --
Rwork0.229 --
obs-26817 99 %
Displacement parametersBiso mean: 92.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→37.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6781 1012 5 11 7809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298074
X-RAY DIFFRACTIONf_angle_d0.535311155
X-RAY DIFFRACTIONf_chiral_restr0.04251226
X-RAY DIFFRACTIONf_plane_restr0.00381284
X-RAY DIFFRACTIONf_dihedral_angle_d14.23374645

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