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- PDB-5t5c: A Novel domain in human EXOG converts apoptotic endonuclease to D... -

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Basic information

Entry
Database: PDB / ID: 5t5c
TitleA Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme
Components
  • DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')
  • Nuclease EXOG, mitochondrial
KeywordsHYDROLASE/DNA / mitochondria / exonuclease / DNA-repair / complex / HYDROLASE-DNA 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
DNA / Nuclease EXOG, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA launch vector pDE-GFP2 (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsSzymanski, M.R. / Yin, W.Y.
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 30, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_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.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
Revision 1.2Oct 16, 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
C: DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
D: DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')
E: DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')
F: DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,5448
Polymers83,4966
Non-polymers492
Water4,864270
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.499, 80.267, 139.177
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 36275.152 Da / Num. of mol.: 2 / Fragment: UNP residues 59-358
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: DNA chain DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')


Mass: 2731.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)
#3: DNA chain DNA (5'-D(P*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DNA launch vector pDE-GFP2 (others)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 2K MME, 10mM MgCl2, 0.1M Na Acetate pH 4.6, 0.2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 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 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 70495 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Χ2: 1.39 / Net I/av σ(I): 31.569 / Net I/σ(I): 8.2 / Num. measured all: 505427
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.85-1.886.334570.8520.4330.78699.1
1.88-1.926.834580.870.4040.81299.70.983
1.92-1.957.134780.9160.3190.8661000.7870.85
1.95-1.997.234990.9460.2350.9161000.5850.632
1.99-2.047.434850.9560.2070.95599.90.5220.562
2.04-2.087.434680.970.1821.0121000.4570.493
2.08-2.147.434870.9750.1491.0451000.3770.406
2.14-2.197.435020.9780.131.0821000.3280.353
2.19-2.267.435090.980.1111.1271000.2790.301
2.26-2.337.434820.9880.0921.1521000.2330.251
2.33-2.417.435280.9880.0791.2231000.1990.215
2.41-2.517.434940.9930.0671.3071000.1690.182
2.51-2.637.335310.9940.0561.3631000.1420.152
2.63-2.767.335250.9940.0481.4841000.1220.132
2.76-2.947.335390.9960.0381.7221000.0950.103
2.94-3.167.335260.9980.0312.0081000.0790.085
3.16-3.487.135780.9980.0262.4991000.0660.071
3.48-3.997.135690.9980.0232.6981000.0570.062
3.99-5.026.936190.9990.0172.0471000.0410.045
5.02-506.737610.9990.0141.56298.80.0320.035

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Processing

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

3ism


Resolution: 1.851→39.231 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.76 / Stereochemistry target values: ML
Details: Authors state that "The high RSRZ score is resulted from DNA-binding induced domain disorder. Please refer the publication for details."
RfactorNum. reflection% reflection
Rfree0.2157 6555 10.01 %
Rwork0.1856 58925 -
obs0.1886 65480 92.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 212.5 Å2 / Biso mean: 59.5935 Å2 / Biso min: 21.13 Å2
Refinement stepCycle: final / Resolution: 1.851→39.231 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4752 658 2 270 5682
Biso mean--31.94 45.54 -
Num. residues----624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075600
X-RAY DIFFRACTIONf_angle_d0.7877712
X-RAY DIFFRACTIONf_chiral_restr0.053838
X-RAY DIFFRACTIONf_plane_restr0.005890
X-RAY DIFFRACTIONf_dihedral_angle_d16.3293258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8511-1.87210.33121540.29321363151764
1.8721-1.89420.34011790.2911586176577
1.8942-1.91730.32641770.29581668184578
1.9173-1.94150.28761880.24391676186480
1.9415-1.96710.25831950.23191759195484
1.9671-1.9940.24621990.22681814201386
1.994-2.02250.26492060.22251865207189
2.0225-2.05270.26112180.21591899211789
2.0527-2.08480.25682070.20411852205989
2.0848-2.1190.24322210.19791905212691
2.119-2.15550.23852080.19141938214692
2.1555-2.19470.2232110.19551954216593
2.1947-2.23690.23212240.1891996222094
2.2369-2.28250.1992220.17941954217694
2.2825-2.33220.22192280.18712013224195
2.3322-2.38640.192250.19241983220895
2.3864-2.44610.21092260.17682044227096
2.4461-2.51220.23612250.1782013223896
2.5122-2.58610.19372280.1892085231397
2.5861-2.66960.23042300.18532071230198
2.6696-2.7650.22532330.19572078231198
2.765-2.87560.21722290.19392097232698
2.8756-3.00650.23722320.19652095232799
3.0065-3.16490.21732360.20162127236399
3.1649-3.36310.22122360.186321452381100
3.3631-3.62260.20272380.172921382376100
3.6226-3.98680.19332390.166421542393100
3.9868-4.5630.18172430.145421822425100
4.563-5.7460.17942450.162322092454100
5.746-39.23980.23822530.20552262251598
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)
15.97882.69960.01052.2513-0.28781.1374-0.17380.8308-0.0148-0.23450.2325-0.0357-0.0128-0.0104-0.03620.25320.02870.01670.38230.08860.258519.5026-4.1575-31.7595
23.29370.1309-0.96112.2647-0.33922.21110.11230.36630.5584-0.11690.0098-0.2564-0.43940.2656-0.10360.2942-0.03640.02290.31390.11680.350533.53737.4914-26.7302
34.2740.3885-0.46812.6328-0.13422.54550.06280.05420.0711-0.0297-0.1016-0.4946-0.22650.5064-0.01420.2104-0.0556-0.00820.34070.10610.352142.1656-0.2567-22.9112
42.668-0.39670.72533.454-4.10015.63660.1232-0.28280.20220.3568-0.1823-0.36330.01480.2712-0.01610.2898-0.0343-0.06130.28440.06150.183125.0038-10.1599-7.8092
53.39030.5659-0.24472.6275-0.27521.6575-0.01110.1099-0.6762-0.1335-0.0726-0.82640.07820.5710.0510.22220.0260.03790.41550.10210.530842.7245-11.0455-23.4692
66.13242.7199-2.69412.9981-2.38553.7508-0.09810.25031.42330.35890.38040.3141-1.05-0.0396-0.23670.8957-0.3318-0.30430.86350.2761.103154.415316.2044-15.3893
74.69261.4791-1.99532.0047-4.73922.69180.1638-0.4088-0.0201-1.1583-0.6328-1.5256-0.20620.39010.24311.5879-0.2795-0.08751.3388-0.02710.927662.510716.3974-22.7863
82.42650.1336-0.14941.87290.00171.58580.02960.4575-0.4326-0.10130.020.05970.2522-0.0304-0.04840.2460.0149-0.02360.3067-0.00470.240315.1375-21.8604-26.6356
91.71710.05210.19791.6096-0.25921.3650.08220.1216-0.14440.05430.05820.25150.1297-0.2343-0.11760.2138-0.00630.02130.31040.0890.21235.0481-16.3696-20.096
103.0720.26010.78982.6309-0.47932.0838-0.026-0.04910.39840.19890.11320.5299-0.3133-0.2809-0.06550.2670.05830.0480.34380.10550.3611-0.4452-6.0785-19.9599
116.53031.77552.16492.3789-0.43575.8487-0.10540.5729-0.49840.18430.43220.36250.8854-0.3408-0.30170.572-0.07290.10740.60050.03670.4123-10.1909-33.9435-8.3091
128.1918-0.65660.53716.89791.30835.54290.5591.27730.1188-1.36650.03541.13010.5937-0.7838-0.14340.8862-0.2639-0.04640.83990.01590.5966-17.0589-38.25-12.1243
132.332-0.81870.47226.65954.25833.77540.4396-0.43271.12340.5568-0.5016-0.1015-1.211-0.5407-0.06160.83-0.09240.03770.5362-0.03430.698436.485618.4576-14.2842
144.3292-3.97773.63193.7063-3.27213.3363-0.3674-0.69141.63720.1285-0.3298-0.909-1.17510.19430.76971.3114-0.0694-0.19910.722-0.02710.887537.56621.2567-15.169
150.83181.321-1.52815.6251-0.02024.47170.3669-0.5779-1.48950.4826-0.0380.25320.870.5395-0.18930.5984-0.0452-0.09550.52380.27130.75867.4221-36.6482-11.3951
164.7906-2.1928-5.12211.79481.7877.3395-1.1905-0.0305-2.17871.16410.37970.11762.1462-0.20010.77870.9832-0.07350.02870.52720.12541.16116.1315-39.502-12.1052
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 61 through 89 )A61 - 89
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 158 )A90 - 158
3X-RAY DIFFRACTION3chain 'A' and (resid 159 through 199 )A159 - 199
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 219 )A200 - 219
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 303 )A220 - 303
6X-RAY DIFFRACTION6chain 'A' and (resid 304 through 335 )A304 - 335
7X-RAY DIFFRACTION7chain 'A' and (resid 336 through 356 )A336 - 356
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 136 )B61 - 136
9X-RAY DIFFRACTION9chain 'B' and (resid 137 through 244 )B137 - 244
10X-RAY DIFFRACTION10chain 'B' and (resid 245 through 303 )B245 - 303
11X-RAY DIFFRACTION11chain 'B' and (resid 304 through 335 )B304 - 335
12X-RAY DIFFRACTION12chain 'B' and (resid 336 through 356 )B336 - 356
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 8 )C1 - 8
14X-RAY DIFFRACTION14chain 'D' and (resid 3 through 10 )D3 - 10
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 8 )E1 - 8
16X-RAY DIFFRACTION16chain 'F' and (resid 3 through 10 )F3 - 10

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