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- PDB-5t3v: A Novel domain in human EXOG converts apoptotic endonuclease to D... -

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Basic information

Entry
Database: PDB / ID: 5t3v
TitleA Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme
ComponentsNuclease EXOG, mitochondrial
KeywordsHYDROLASE / mitochondria / exonuclease / DNA-repair / 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 / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix ...Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters / apoptotic DNA fragmentation / single-stranded DNA endodeoxyribonuclease activity / Strand-asynchronous mitochondrial DNA replication / 5'-3' exonuclease activity / RNA endonuclease activity / endonuclease activity / nucleic acid binding / mitochondrial inner membrane / mitochondrial matrix / protein-containing complex / mitochondrion / metal ion binding / nucleus
Similarity search - Function
EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / 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 ...EXOG, C-terminal / Endo/exonuclease (EXOG) C-terminal domain / 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
: / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSzymanski, M.R. / Yin, W.Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 083703 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 110591 United States
CitationJournal: Nat Commun / Year: 2017
Title: A domain in human EXOG converts apoptotic endonuclease to DNA-repair exonuclease.
Authors: Szymanski, M.R. / Yu, W. / Gmyrek, A.M. / White, M.A. / Molineux, I.J. / Lee, J.C. / Yin, Y.W.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclease EXOG, mitochondrial
B: Nuclease EXOG, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9866
Polymers72,6842
Non-polymers3024
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-77 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.340, 83.436, 74.771
Angle α, β, γ (deg.)90.000, 113.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nuclease EXOG, mitochondrial / Endonuclease G-like 1 / Endo G-like 1


Mass: 36342.219 Da / Num. of mol.: 2 / Fragment: UNP residues 59-368
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXOG, ENDOGL1, ENDOGL2, ENGL / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2C4, Hydrolases; Acting on ester bonds; Endoribonucleases that are active with either ribo- or deoxyribonucleic acids and produce 5'-phosphomonoesters
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.06 Å3/Da / Density % sol: 59.81 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 2M (NH4)2SO4, 0.1M MgCl2, 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.89 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.6→49.708 Å / Num. obs: 24211 / % possible obs: 95.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 21.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISM

3ism


Resolution: 2.6→49.708 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.96
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 1993 8.23 %8.21%
Rwork0.1758 ---
obs0.1798 24211 94.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.79 Å2 / Biso mean: 69.9715 Å2 / Biso min: 24.48 Å2
Refinement stepCycle: final / Resolution: 2.6→49.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 12 81 4910
Biso mean--127.37 48.3 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034941
X-RAY DIFFRACTIONf_angle_d0.4836685
X-RAY DIFFRACTIONf_chiral_restr0.043717
X-RAY DIFFRACTIONf_plane_restr0.003869
X-RAY DIFFRACTIONf_dihedral_angle_d13.1322993
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5999-2.66490.31361300.25071461159188
2.6649-2.7370.34261390.24171502164191
2.737-2.81750.33581390.25581550168992
2.8175-2.90840.29931310.24851545167693
2.9084-3.01240.27721460.22211560170694
3.0124-3.1330.25991380.21421575171395
3.133-3.27550.2691450.20661598174395
3.2755-3.44820.29621430.20431593173696
3.4482-3.66420.22281350.17441616175196
3.6642-3.9470.19761520.15051602175497
3.947-4.3440.18211440.13621637178197
4.344-4.9720.15391460.12151634178097
4.972-6.26230.1911480.15111662181098
6.2623-49.7170.2241570.18731683184098
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.9692-0.4322.04632.76240.16092.9859-0.2130.02450.249-0.2660.1605-0.01310.0893-0.19710.00080.358-0.00490.0360.26080.00360.3431-12.939128.2775-10.8295
23.9765-0.3871.52138.6637-0.29666.57060.1570.8613-0.1717-0.7666-0.2171-0.05890.09940.09610.0020.47960.0070.05720.5402-0.03160.2626-11.926318.0906-21.8648
32.2167-0.97040.91962.6043-0.68441.9643-0.02430.0142-0.0928-0.22480.07920.24030.0637-0.4306-0.07790.3955-0.0613-0.00990.43340.00420.3569-22.092617.4372-10.37
45.0003-0.31340.98172.6133-0.70442.9873-0.1466-1.0160.06240.23620.11650.2693-0.0625-0.55980.03750.41770.01350.03370.68120.04480.4138-29.841921.51940.8341
55.9948-1.14131.60580.5604-0.96387.69510.33190.4029-0.7494-0.0976-0.22690.22460.2437-0.7089-0.11610.5906-0.0537-0.05880.6389-0.09320.5162-41.894410.301-29.3493
63.6819-0.50630.60721.6701-0.13471.3414-0.26-0.62570.64650.29740.0868-0.1852-0.1681-0.15320.15570.41060.0502-0.0360.3926-0.12160.5078-0.119528.2824.5224
74.5042-0.87240.63953.4742-0.272.8485-0.0771-1.36180.06040.54430.04590.0314-0.1264-0.30190.05240.50420.07220.02090.6671-0.01780.3128-1.511718.768316.6265
84.43820.1170.42472.0906-0.2141.3314-0.0834-0.01460.1108-0.02440.0301-0.2668-0.01030.21890.0370.35730.0406-0.01030.3152-0.0080.360411.539617.31580.6113
95.36441.1546-0.36475.41824.0173.27390.2450.0889-0.2617-0.2518-0.17410.0428-0.7233-0.41470.08880.6420.0687-0.08330.5030.01950.527224.54339.638117.0469
103.31040.3489-0.0696.01594.49663.39170.0722-0.3522-0.11180.28260.0775-0.10610.6507-0.4579-0.25990.66140.0328-0.07920.67790.0330.540729.01078.664827.3788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 108 )A60 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 136 )A109 - 136
3X-RAY DIFFRACTION3chain 'A' and (resid 137 through 235 )A137 - 235
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 303 )A236 - 303
5X-RAY DIFFRACTION5chain 'A' and (resid 304 through 358 )A304 - 358
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 108 )B59 - 108
7X-RAY DIFFRACTION7chain 'B' and (resid 109 through 136 )B109 - 136
8X-RAY DIFFRACTION8chain 'B' and (resid 137 through 303 )B137 - 303
9X-RAY DIFFRACTION9chain 'B' and (resid 304 through 318 )B304 - 318
10X-RAY DIFFRACTION10chain 'B' and (resid 319 through 358 )B319 - 358

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