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- PDB-5gkc: The crystal structure of the CPS-6 H148A/F122A -

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Basic information

Entry
Database: PDB / ID: 5gkc
TitleThe crystal structure of the CPS-6 H148A/F122A
ComponentsEndonuclease G, mitochondrial
KeywordsHYDROLASE / mitochondria / H148A / F122A mutation / DNA/RNA binding
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 / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 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 / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / 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
Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsLin, J.L. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica and the National Science Council, Taiwan, R.O.C Taiwan
CitationJournal: 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.
History
DepositionJul 4, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)57,3952
Polymers57,3952
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-15 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.614, 45.630, 80.988
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number4
Space group name H-MP1211

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.26 Å3/Da / Density % sol: 45.63 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging 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: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2015
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: 1.892→27.535 Å / Num. obs: 40272 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rsym value: 0.07 / Net I/σ(I): 16.8
Reflection shellResolution: 1.89→1.92 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1059refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5B

3s5b


Resolution: 1.892→27.535 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.69
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 2029 5.4 %24.9
Rwork0.1984 ---
obs0.2011 37561 90 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.4 Å2
Refinement stepCycle: LAST / Resolution: 1.892→27.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 2 401 4257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073949
X-RAY DIFFRACTIONf_angle_d1.1525333
X-RAY DIFFRACTIONf_dihedral_angle_d14.1421479
X-RAY DIFFRACTIONf_chiral_restr0.081568
X-RAY DIFFRACTIONf_plane_restr0.005691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8917-1.9390.2898950.211663X-RAY DIFFRACTION31
1.939-1.99140.23141080.20591880X-RAY DIFFRACTION35
1.9914-2.050.23931170.20462048X-RAY DIFFRACTION39
2.05-2.11610.29751310.20472303X-RAY DIFFRACTION43
2.1161-2.19170.29331430.21142478X-RAY DIFFRACTION47
2.1917-2.27940.25381530.20362696X-RAY DIFFRACTION50
2.2794-2.38310.25131550.20912709X-RAY DIFFRACTION51
2.3831-2.50870.30041550.20942708X-RAY DIFFRACTION51
2.5087-2.66570.29731560.21342720X-RAY DIFFRACTION51
2.6657-2.87130.28081560.21412732X-RAY DIFFRACTION52
2.8713-3.15990.25971560.21212729X-RAY DIFFRACTION52
3.1599-3.61630.20941590.18682780X-RAY DIFFRACTION52
3.6163-4.55280.20431630.172830X-RAY DIFFRACTION53
4.5528-27.53820.24271820.19653256X-RAY DIFFRACTION61

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