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- PDB-3s5b: Crystal Structure of CED-3 Protease Suppressor-6 (CPS-6) from Cae... -

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Basic information

Entry
Database: PDB / ID: 3s5b
TitleCrystal Structure of CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans
ComponentsEndonuclease G
KeywordsHYDROLASE / DNA fragmentation / Nuclease / DNase / protein-DNA interactions / beta-beta-alpha-metal finger nuclease / Mitochondria
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 / endonuclease activity / sequence-specific DNA binding ...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 / endonuclease activity / sequence-specific DNA binding / mitochondrial inner membrane / protein homodimerization activity / mitochondrion / nucleus / metal ion binding
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 / molecular replacement / Resolution: 1.796 Å
AuthorsYuan, H.S. / Lin, J.L.J.
CitationJournal: 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. / Lin, C.L. / Hsiao, Y.Y. / Yang, W.Z. / Wang, Y.T. / Doudeva, L.G. / Skeen-Gaar, R.R. / Xue, D. / Yuan, H.S.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 / _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
B: Endonuclease G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2404
Polymers57,1912
Non-polymers492
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-2 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.221, 45.379, 80.310
Angle α, β, γ (deg.)90.000, 104.170, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endonuclease G / CPS-6 / Endo G / Ced-3 protease suppressor 6


Mass: 28595.586 Da / Num. of mol.: 2 / Fragment: residues 63-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: cps-6 / Plasmid: pQE30 / 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: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.14 Å3/Da / Density % sol: 42.48 % / Mosaicity: 0.579 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 6% Tacsimate, 0.1M MES, 25% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 31, 2010
RadiationMonochromator: double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.796→50 Å / Num. all: 83591 / Num. obs: 44074 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.085 / Χ2: 2.233 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.832.90.34822332.0371100
1.83-1.8630.29222501.8199.9
1.86-1.930.31122362.306199.9
1.9-1.942.90.322323.16198.9
1.94-1.9830.21322642.576199.9
1.98-2.0330.17922261.979199.9
2.03-2.082.90.21122403.081198.9
2.08-2.1330.15222272.064199.9
2.13-2.230.13122811.776199.9
2.2-2.272.90.15522082.909198.3
2.27-2.3530.12122502.2831100
2.35-2.4430.11822722.624199.9
2.44-2.5530.09822512.226199.9
2.55-2.692.90.09822722.81199.7
2.69-2.8630.07622632.312199.6
2.86-3.0830.06722582.178199.7
3.08-3.3930.04722651.806199.4
3.39-3.882.70.04314401.986163
3.88-4.882.90.03220861.559189.8
4.88-502.90.02723201.154197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.796→37.593 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8816 / SU ML: 0.19 / σ(F): 0.08 / Phase error: 19.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2099 1876 4.55 %RANDOM
Rwork0.1659 ---
obs0.168 41201 90.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.36 Å2 / ksol: 0.418 e/Å3
Displacement parametersBiso max: 77.92 Å2 / Biso mean: 16.762 Å2 / Biso min: 0.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.1145 Å20 Å21.5997 Å2
2---2.9635 Å20 Å2
3---3.078 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.796→37.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3836 0 2 430 4268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073933
X-RAY DIFFRACTIONf_angle_d1.0435314
X-RAY DIFFRACTIONf_chiral_restr0.076567
X-RAY DIFFRACTIONf_plane_restr0.005687
X-RAY DIFFRACTIONf_dihedral_angle_d14.0141441
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7958-1.84430.23791300.16052784291484
1.8443-1.89860.23911450.17112864300987
1.8986-1.95990.24441410.18472877301886
1.9599-2.02990.19781400.15113023316392
2.0299-2.11120.22441450.16313069321492
2.1112-2.20720.18751460.15543073321993
2.2072-2.32360.27941420.17743051319391
2.3236-2.46910.21931540.16413163331795
2.4691-2.65970.24071480.17063209335795
2.6597-2.92730.20271540.17763235338997
2.9273-3.35070.18951590.16173265342498
3.3507-4.22060.17861120.14182370248270
4.2206-37.60080.18011600.16663342350296
Refinement TLS params.Method: refined / Origin x: 27.3766 Å / Origin y: -2.8635 Å / Origin z: 20.2631 Å
111213212223313233
T0.0052 Å20.0065 Å20.0196 Å2--0.0033 Å20.0136 Å2--0.0016 Å2
L0.6276 °20.1418 °20.1349 °2-0.6281 °20.0641 °2--0.4194 °2
S-0.0038 Å °0.043 Å °0.0737 Å °-0.021 Å °0.0167 Å °0.0283 Å °-0.0195 Å °-0.0207 Å °-0.0096 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA63 - 303
2X-RAY DIFFRACTION1allB60 - 302
3X-RAY DIFFRACTION1allA1
4X-RAY DIFFRACTION1allB1
5X-RAY DIFFRACTION1allA4 - 470
6X-RAY DIFFRACTION1allB2 - 516

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