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- PDB-5gkp: Crystal structure of the EndoG worm homologue CPS-6 H148A/F122A i... -

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Basic information

Entry
Database: PDB / ID: 5gkp
TitleCrystal structure of the EndoG worm homologue CPS-6 H148A/F122A in complex with DNA
Components
  • DNA (5'-D(*TP*TP*TP*TP*T)-3')
  • Endonuclease G, mitochondrial
KeywordsHYDROLASE/DNA / EndoG / mitochondria / endonuclease / non-specific nuclease / protein-DNA interactions / 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 / double-stranded DNA endonuclease activity / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / mitochondrial intermembrane space / endonuclease activity ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / double-stranded DNA endonuclease activity / single-stranded DNA endodeoxyribonuclease activity / apoptotic DNA fragmentation / DNA catabolic process / RNA catabolic process / RNA endonuclease activity / DNA endonuclease activity / mitochondrial intermembrane space / endonuclease activity / sequence-specific DNA binding / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / metal ion binding / nucleus
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 speciesCaenorhabditis elegans (invertebrata)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLin, J.L. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica and the National Science Council, Taiwan Taiwan
Citation
Journal: Nucleic Acids Res. / Year: 2016
Title: Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.
Authors: Lin, J.L. / Wu, C.C. / Yang, W.Z. / Yuan, H.S.
#1: Journal: J.BIOL.CHEM. / Year: 2012
Title: StructuralInsightsintoApoptoticDNADegradationbyCED-3 ProteaseSuppressor-6(CPS-6)fromCaenorhabditiselegans
Authors: Lin, J.L. / Yuan, H.S.
History
DepositionJul 5, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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

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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: DNA (5'-D(*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*TP*TP*TP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2716
Polymers62,2234
Non-polymers492
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.672, 72.562, 127.914
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 Endonuclease G, mitochondrial / Endo G / Ced-3 protease suppressor 6


Mass: 28697.721 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 63-305 / Mutation: H148A, F122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cps-6, C41D11.8 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q95NM6, 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(*TP*TP*TP*TP*T)-3')


Mass: 2413.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 30% PEG 1000

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 6, 2014
Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 25101 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 23.1
Reflection shellResolution: 2.27→2.35 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5B

3s5b


Resolution: 2.3→19.783 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.5
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2525 2042 8.26 %
Rwork0.1735 --
obs0.1801 24707 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 194 2 175 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144104
X-RAY DIFFRACTIONf_angle_d1.4265578
X-RAY DIFFRACTIONf_dihedral_angle_d16.8491547
X-RAY DIFFRACTIONf_chiral_restr0.058600
X-RAY DIFFRACTIONf_plane_restr0.007688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.31990.2411960.20741068X-RAY DIFFRACTION37
2.3199-2.37780.27991120.20531250X-RAY DIFFRACTION44
2.3778-2.4420.32341290.19041437X-RAY DIFFRACTION50
2.442-2.51370.29221350.18691498X-RAY DIFFRACTION52
2.5137-2.59470.27311350.18521516X-RAY DIFFRACTION53
2.5947-2.68720.27861390.19511538X-RAY DIFFRACTION53
2.6872-2.79450.31141350.1891503X-RAY DIFFRACTION53
2.7945-2.92130.26461370.18841522X-RAY DIFFRACTION53
2.9213-3.07480.2431360.19061521X-RAY DIFFRACTION53
3.0748-3.26660.27931390.19561532X-RAY DIFFRACTION53
3.2666-3.51750.25721380.1681538X-RAY DIFFRACTION53
3.5175-3.86910.26221390.16741551X-RAY DIFFRACTION54
3.8691-4.42350.21761400.14331556X-RAY DIFFRACTION54
4.4235-5.55270.20721470.1391612X-RAY DIFFRACTION56
5.5527-19.78360.23691850.18592023X-RAY DIFFRACTION70

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