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- PDB-9m1e: Crystal structure of the CPS-6 H148A/F122A versus cis-resveratrol... -

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Basic information

Entry
Database: PDB / ID: 9m1e
TitleCrystal structure of the CPS-6 H148A/F122A versus cis-resveratrol complex
ComponentsEndonuclease G, mitochondrial
KeywordsDNA BINDING PROTEIN / complex / mitochondrial and endoribonuclease
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, 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
RESVERATROL / Endonuclease G, mitochondrial
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsLin, L.J. / Yuan, H.S.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-IA-110-L02 Taiwan
Citation
Journal: to be published
Title: Crystal structure of the CPS-6 H148A/F122A versus cis-resveratrol complex
Authors: Lin, L.J. / Yuan, H.S.
#1: 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, L.J. / Wu, C.C. / Yang, W.Z. / Yuan, H.S.
History
DepositionFeb 25, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3578
Polymers57,3952
Non-polymers9626
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-18 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.661, 45.856, 81.003
Angle α, β, γ (deg.)90.00, 102.81, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: F122A and H148A
Source method: isolated from a genetically manipulated source
Details: N-terminal 6xhistidine tagged / Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: cps-6, C41D11.8 / Plasmid: pQE30 / Details (production host): ampicillin resistant / Production host: Escherichia coli M15 (bacteria)
References: UniProt: Q95NM6, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical
ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H12O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.6 % / Description: thin plate shape
Crystal growTemperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100 mM HEPES, 30% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.62 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Sep 20, 2017 / Details: A Si(111) double-crystal monochromator (DCM)
RadiationMonochromator: LN2 cooled Si(111) double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.62 Å / Relative weight: 1
ReflectionResolution: 2.99→29.93 Å / Num. obs: 10238 / % possible obs: 99.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 60.77 Å2 / Rpim(I) all: 0.102 / Rrim(I) all: 0.196 / Rsym value: 0.158 / Net I/σ(I): 7.3
Reflection shellResolution: 3→3.11 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 286093 / Rpim(I) all: 0.313 / Rrim(I) all: 0.573 / Rsym value: 0.456 / Χ2: 0.874 / % possible all: 98

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Processing

Software
NameVersionClassification
HKL-2000V 706data collection
HKL-2000V 706data reduction
HKL-2000V 706data scaling
PHENIX1.12-2829model building
PHENIX1.12-2829phasing
PHENIX1.12-2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GKP

5gkp


Resolution: 2.99→29.9 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2845 998 10 %
Rwork0.1724 --
obs0.1839 9976 94.03 %
Refinement stepCycle: LAST / Resolution: 2.99→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 70 4 3898

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