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- PDB-5zki: Human EXOG-H140A in complex with duplex DNA -

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Basic information

Entry
Database: PDB / ID: 5zki
TitleHuman EXOG-H140A in complex with duplex DNA
Components
  • DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
  • Nuclease EXOG, mitochondrial
KeywordsHYDROLASE/DNA / Enzyme-substrate complex / Mitochondrial exonuclease / HYDROLASE-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 / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix / 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, 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
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: 2.321 Å
AuthorsWu, C.C. / Lin, J.L.J. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: A unique exonuclease ExoG cleaves between RNA and DNA in mitochondrial DNA replication.
Authors: Wu, C.C. / Lin, J.L.J. / Yang-Yen, H.F. / Yuan, H.S.
History
DepositionMar 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / 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
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id
Revision 1.4Oct 23, 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: Nuclease EXOG, mitochondrial
C: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
D: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
F: DNA (5'-D(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')
B: Nuclease EXOG, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,23011
Polymers93,0866
Non-polymers1445
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12480 Å2
ΔGint-112 kcal/mol
Surface area33350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.497, 91.123, 129.451
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 39216.262 Da / Num. of mol.: 2 / Mutation: H140A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS
References: UniProt: Q9Y2C4, 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(*CP*GP*GP*GP*AP*TP*AP*TP*CP*CP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M BIS-Tris pH 6.5, 20% w/v PEG 1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 1, 2017
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 38137 / % possible obs: 99.8 % / Redundancy: 7 % / CC1/2: 0.986 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.999 / Net I/σ(I): 19.49
Reflection shellResolution: 2.32→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.794 / Num. unique obs: 2468 / CC1/2: 0.935 / Rpim(I) all: 0.194 / Rrim(I) all: 0.517 / Χ2: 1.005 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4A1N

4a1n


Resolution: 2.321→29.619 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 1908 5.02 %Random selection
Rwork0.1797 ---
obs0.1816 38038 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.321→29.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4845 972 5 111 5933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036120
X-RAY DIFFRACTIONf_angle_d0.5158486
X-RAY DIFFRACTIONf_dihedral_angle_d16.0063536
X-RAY DIFFRACTIONf_chiral_restr0.042921
X-RAY DIFFRACTIONf_plane_restr0.003940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3212-2.37920.28431350.22732390X-RAY DIFFRACTION94
2.3792-2.44350.26671450.20622553X-RAY DIFFRACTION100
2.4435-2.51530.29121320.2152541X-RAY DIFFRACTION100
2.5153-2.59650.30051240.21552574X-RAY DIFFRACTION100
2.5965-2.68920.2421190.19782576X-RAY DIFFRACTION100
2.6892-2.79680.28091380.20042575X-RAY DIFFRACTION100
2.7968-2.9240.24141430.18552576X-RAY DIFFRACTION100
2.924-3.0780.24951490.17842552X-RAY DIFFRACTION100
3.078-3.27060.20651270.18132591X-RAY DIFFRACTION100
3.2706-3.52280.19531350.16812587X-RAY DIFFRACTION100
3.5228-3.87660.19651370.16572614X-RAY DIFFRACTION100
3.8766-4.43590.18791400.1622602X-RAY DIFFRACTION100
4.4359-5.58270.20311500.16162648X-RAY DIFFRACTION100
5.5827-29.62090.22051340.19852751X-RAY DIFFRACTION99

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