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- PDB-5t4i: A Novel domain in human EXOG converts apoptotic endonuclease to D... -

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Basic information

Entry
Database: PDB / ID: 5t4i
TitleA Novel domain in human EXOG converts apoptotic endonuclease to DNA-repair enzyme
Components
  • DNA (5'-D(*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*CP*GP*TP*GP*C)-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: 2.389 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 29, 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 1.2Nov 13, 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(*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(*GP*CP*AP*CP*GP*TP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6058
Polymers83,4966
Non-polymers1102
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.508, 79.723, 138.870
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(*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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 22% PEG 2000 MM 0.2M (NH4)2SO4, 0.1M Na Acetate pH 4.6 100mM MnCl2

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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: Jun 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.89 Å / Relative weight: 1
ReflectionResolution: 2.389→50 Å / Num. obs: 32857 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 45.49 Å2 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.052 / Rrim(I) all: 0.126 / Χ2: 1.836 / Net I/av σ(I): 24.786 / Net I/σ(I): 8.2 / Num. measured all: 352305
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.389-2.444.40.6380.792197.4
2.44-2.494.70.6560.841199.6
2.49-2.5350.6310.851199.8
2.53-2.595.30.5980.874199.8
2.59-2.645.60.5240.91199.9
2.64-2.75.90.5280.915199.6
2.7-2.7760.4560.931199.6
2.77-2.8560.3740.95199.3
2.85-2.9360.2940.963199.4
2.93-3.025.90.2480.971199.4
3.02-3.135.90.2140.988199.2
3.13-3.265.80.1730.985199.5
3.26-3.415.80.1390.991199.2
3.41-3.585.80.1150.99199.5
3.58-3.815.80.1040.991199.9
3.81-4.15.80.0890.993199.9
4.1-4.525.80.080.9941100
4.52-5.175.90.0710.9951100
5.17-6.516.20.0690.9951100
6.51-506.20.0570.997199.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T40

5t40


Resolution: 2.389→40.031 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.41
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
Rfree0.2287 1982 6.09 %
Rwork0.1905 --
obs0.1928 32548 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 204.22 Å2 / Biso mean: 67.988 Å2 / Biso min: 25.71 Å2
Refinement stepCycle: final / Resolution: 2.389→40.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4771 734 2 53 5560
Biso mean--57.31 47.82 -
Num. residues----631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035705
X-RAY DIFFRACTIONf_angle_d0.5267871
X-RAY DIFFRACTIONf_chiral_restr0.042855
X-RAY DIFFRACTIONf_plane_restr0.003897
X-RAY DIFFRACTIONf_dihedral_angle_d16.8873309
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 (%)
2.3889-2.44860.35011190.25661968208790
2.4486-2.51480.25341390.24482114225397
2.5148-2.58880.28671550.24312126228198
2.5888-2.67230.27561300.22922171230198
2.6723-2.76780.25791440.23212127227198
2.7678-2.87860.25551400.22812163230399
2.8786-3.00960.21441370.20722197233499
3.0096-3.16820.26521360.20892184232099
3.1682-3.36660.25451370.20042189232699
3.3666-3.62640.21421520.180922242376100
3.6264-3.9910.23051450.173522152360100
3.991-4.56780.19461440.160422412385100
4.5678-5.75220.19551460.16722722418100
5.7522-40.03690.22691580.186223752533100
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)
16.03683.31452.62843.26922.13751.7322-0.11640.59770.3068-0.24440.1778-0.03840.11790.20840.00780.43450.0375-0.00820.47470.01970.3913-15.22076.6708-34.9894
24.0125-0.36740.98925.11291.29172.82850.1050.3461-0.3358-0.0127-0.0450.29480.3886-0.02480.03220.3454-0.02930.03160.3867-0.03690.3011-34.9435-1.2131-29.6162
35.04410.24330.84012.38280.19362.04690.10710.2098-0.3877-0.0403-0.03570.19280.3176-0.2176-0.07330.3329-0.0464-0.00770.2843-0.03360.3191-36.1795-4.8203-23.9722
43.501-0.3273-0.37562.65664.32827.2038-0.0653-0.39650.20090.78220.08730.2664-0.0734-0.1036-0.0840.3662-0.0220.03310.34790.00420.2618-24.936110.1339-7.7087
54.93290.23521.78943.5264-0.69982.8777-0.04160.13010.5402-0.0291-0.0070.7548-0.2808-0.29640.03330.30110.01730.02160.3472-0.06620.4845-42.656810.9859-23.3526
64.8683-0.33341.97987.93194.05313.1095-0.1628-0.5366-0.39650.40360.12650.66980.6562-0.34870.00640.7487-0.1420.07190.6870.1280.7799-53.7099-16.6952-15.748
72.0817-1.5132-1.42336.52884.80933.54460.01180.4232-0.414-0.2247-0.60131.91870.0023-0.88960.62670.9895-0.20810.02380.7780.04131.1719-60.7283-18.9368-19.2838
84.47855.904-2.81057.8462-2.57123.20920.12090.5061-0.27180.04870.0567-0.13470.181-0.1095-0.15230.39310.07140.03080.3961-0.0720.3004-25.248213.7088-35.0565
94.7901-0.5789-1.25853.4469-0.24133.74570.27940.09710.35470.14-0.1106-0.3484-0.14970.081-0.18840.32360.013-0.03470.3748-0.01050.2968-7.346620.2977-27.07
105.4171-0.68210.11472.92310.47345.00760.1682-0.00950.84340.0199-0.08370.1393-0.6284-0.1563-0.14050.38750.01490.0370.27-0.04240.429-15.917928.4305-19.7542
112.80870.6404-0.67762.112-0.28931.80960.05760.08160.00660.07920.0153-0.287600.2001-0.06780.29710.0122-0.04910.3629-0.05410.2779-4.312813.2557-19.7993
123.79124.38624.07347.90448.5179.1314-0.05250.1661-0.48890.24280.7688-1.40390.07190.666-0.81680.3136-0.02950.01820.5288-0.00620.44969.394517.2699-16.905
136.7334-0.38850.36182.1466-3.00957.1127-0.02480.2310.2148-0.18070.1702-0.8042-0.61330.0061-0.17340.8624-0.1928-0.11140.73220.05390.632413.955638.5413-8.7979
141.9011-3.42761.08699.3254-2.06576.123-0.3903-0.48921.7360.78160.5393-0.209-1.1123-0.4295-0.19420.70630.0574-0.04560.5983-0.21660.9675-8.335638.0697-11.6338
156.74-6.08162.22336.7958-2.9986.8812-1.04980.75451.34990.80090.1348-0.2826-1.466-0.73790.83710.91090.0073-0.17450.8791-0.12551.1602-7.466939.6736-12.0582
164.0981-2.8152-3.66155.76642.11743.4030.0351-0.1858-1.9080.91640.12470.51821.20991.1492-0.26190.81980.1488-0.1240.57160.09230.9195-35.1767-20.037-14.5807
179.0994-5.8777-2.84794.25263.34429.3205-0.30350.162-0.07260.4786-0.001-1.17781.53921.0310.30151.02020.0880.27340.82720.10221.2209-35.974-21.7056-15.1421
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 78 )A60 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 108 )A79 - 108
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 199 )A109 - 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 333 )A304 - 333
7X-RAY DIFFRACTION7chain 'A' and (resid 334 through 356 )A334 - 356
8X-RAY DIFFRACTION8chain 'B' and (resid 60 through 79 )B60 - 79
9X-RAY DIFFRACTION9chain 'B' and (resid 80 through 108 )B80 - 108
10X-RAY DIFFRACTION10chain 'B' and (resid 109 through 140 )B109 - 140
11X-RAY DIFFRACTION11chain 'B' and (resid 141 through 286 )B141 - 286
12X-RAY DIFFRACTION12chain 'B' and (resid 287 through 318 )B287 - 318
13X-RAY DIFFRACTION13chain 'B' and (resid 319 through 357 )B319 - 357
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 9 )C1 - 9
15X-RAY DIFFRACTION15chain 'D' and (resid 2 through 10 )D2 - 10
16X-RAY DIFFRACTION16chain 'E' and (resid 1 through 9 )E1 - 9
17X-RAY DIFFRACTION17chain 'F' and (resid 2 through 10 )F2 - 10

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