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- PDB-4qn0: Crystal structure of the CPS-6 mutant Q130K -

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Basic information

Entry
Database: PDB / ID: 4qn0
TitleCrystal structure of the CPS-6 mutant Q130K
ComponentsEndonuclease G, mitochondrial
KeywordsHYDROLASE / beta-beta-alpha metal motif / endoribonuclease / mitochondrial membrane
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: 2.74 Å
AuthorsLin, J.L.J. / Yuan, H.S.
Citation
Journal: Cell Rep / Year: 2016
Title: Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G
Authors: Lin, J.L.J. / Nakagawa, A. / Skeen-Gaar, R. / Yang, W.Z. / Zhao, P. / Zhang, Z. / Ge, X. / Mitani, S. / Xue, D. / Yuan, H.S.
#1: Journal: J.Biol.Chem. / Year: 2012
Title: Structural Insights into Apoptotic DNA Degradation by CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans
Authors: Lin, J.L.J. / Nakagawa, A. / Hsiao, Y.Y. / Yang, W.Z. / Wang, Y.T. / Doudeva, L.G. / Skeen-Gaar, R.R. / Xui, D. / Yuan, H.S.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
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 / struct_ref_seq_dif / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,6878
Polymers109,5894
Non-polymers974
Water3,225179
1
A: Endonuclease G, mitochondrial
C: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8434
Polymers54,7952
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endonuclease G, mitochondrial
D: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8434
Polymers54,7952
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4222
Polymers27,3971
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4222
Polymers27,3971
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4222
Polymers27,3971
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Endonuclease G, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4222
Polymers27,3971
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.550, 122.442, 73.522
Angle α, β, γ (deg.)90.00, 96.02, 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: 27397.334 Da / Num. of mol.: 4 / Fragment: UNP residues 64-302 / Mutation: H148A, Q130K
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)
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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.76 Å3/Da / Density % sol: 55.42 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M sodium citrate tribasic dihydrate, 18% PEG3350 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 8, 2013
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: 2.74→26.48 Å / Num. all: 29545 / Num. obs: 29545 / % possible obs: 99.7 % / Observed criterion σ(I): 4.26 / Redundancy: 3.7 % / Biso Wilson estimate: 27.42 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.077 / Net I/σ(I): 11.49
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.75-2.83.83.2752808990.4451100
2.8-2.853.83.5464480870.4111100
2.85-2.93.84.0918918920.3621100
2.9-2.963.84.4507772020.3311100
2.96-3.033.85.123711340.286199.9
3.03-3.13.85.8731707320.2461100
3.1-3.173.86.5980861240.2131100
3.17-3.263.88.3139013450.173199.7
3.26-3.363.89.451063830.149199.9
3.36-3.463.711.13725490.139199.3
3.46-3.593.712.643410850.11199.7
3.59-3.733.613.384057970.109199.4
3.73-3.93.715.189393940.089199.7
3.9-4.113.717.874125870.071199.9
4.11-4.363.720.613333330.053199.7
4.36-4.73.722.583596210.046198.8
4.7-5.173.822.534545450.046199.8
5.17-5.923.821.80341880.047199.9
5.92-7.463.821.726829270.055199.9
7.46-503.426.314606740.053197.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1059)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S5B

3s5b


Resolution: 2.74→26.48 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 24.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2353 1965 6.65 %
Rwork0.1853 --
obs0.1886 29535 94.48 %
all-29545 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.9 Å2
Refinement stepCycle: LAST / Resolution: 2.74→26.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 4 179 7865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057873
X-RAY DIFFRACTIONf_angle_d0.92710625
X-RAY DIFFRACTIONf_dihedral_angle_d142947
X-RAY DIFFRACTIONf_chiral_restr0.0611130
X-RAY DIFFRACTIONf_plane_restr0.0051371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7404-2.80890.3027930.24561433X-RAY DIFFRACTION68
2.8089-2.88470.30171220.24451597X-RAY DIFFRACTION78
2.8847-2.96950.27711340.24231810X-RAY DIFFRACTION86
2.9695-3.06520.30021330.22691964X-RAY DIFFRACTION94
3.0652-3.17460.25141380.22432065X-RAY DIFFRACTION99
3.1746-3.30150.2781460.2062054X-RAY DIFFRACTION100
3.3015-3.45140.28511520.19852050X-RAY DIFFRACTION99
3.4514-3.6330.24441380.18812090X-RAY DIFFRACTION100
3.633-3.860.24621590.18732087X-RAY DIFFRACTION100
3.86-4.15690.21211550.16042048X-RAY DIFFRACTION100
4.1569-4.57330.1771410.13862090X-RAY DIFFRACTION99
4.5733-5.23070.17591510.14222085X-RAY DIFFRACTION100
5.2307-6.57340.22561500.17252081X-RAY DIFFRACTION100
6.5734-26.48670.20411530.17982116X-RAY DIFFRACTION99

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