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- PDB-6ozr: Crystal structure of Mus musculus (Mm) Endonuclease V in complex ... -

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Basic information

Entry
Database: PDB / ID: 6ozr
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mg2+
Components
  • DNA/RNA (23-MER)
  • Endonuclease V
KeywordsHYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
Function / homology
Function and homology information


DNA endonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / cytoplasmic stress granule / single-stranded RNA binding / DNA repair / nucleolus / magnesium ion binding / DNA binding / cytoplasm
Similarity search - Function
Endonuclease V / Endonuclease V / archaeoglobus fulgidus dsm 4304 fold / archaeoglobus fulgidus dsm 4304 superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / DNA/RNA hybrid / DNA/RNA hybrid (> 10) / Endonuclease V
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSamara, N.L. / Yang, W.
CitationJournal: Mol.Cell / Year: 2019
Title: Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Authors: Wu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.
History
DepositionMay 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Mar 13, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endonuclease V
B: Endonuclease V
C: DNA/RNA (23-MER)
D: DNA/RNA (23-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,04221
Polymers70,6844
Non-polymers1,35817
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-72 kcal/mol
Surface area24960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.078, 72.663, 154.574
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / DNA/RNA hybrid , 2 types, 4 molecules ABCD

#1: Protein Endonuclease V


Mass: 28048.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Endov / Production host: Escherichia coli (E. coli)
References: UniProt: Q8C9A2, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: DNA/RNA hybrid DNA/RNA (23-MER)


Mass: 7293.379 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 7 types, 296 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M potassium sodium tartrate, 20-25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 24, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 43769 / % possible obs: 97.3 % / Redundancy: 7.6 % / Net I/σ(I): 19.4
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 1694

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→35.368 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.36
RfactorNum. reflection% reflection
Rfree0.1942 2198 5.03 %
Rwork0.1577 --
obs0.1595 43692 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→35.368 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 630 84 279 4807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074865
X-RAY DIFFRACTIONf_angle_d0.946727
X-RAY DIFFRACTIONf_dihedral_angle_d16.7582887
X-RAY DIFFRACTIONf_chiral_restr0.055788
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1499-2.19660.22981040.20632002X-RAY DIFFRACTION76
2.1966-2.24770.2511390.20732395X-RAY DIFFRACTION91
2.2477-2.30390.25331250.20142516X-RAY DIFFRACTION96
2.3039-2.36620.25421420.18852562X-RAY DIFFRACTION98
2.3662-2.43580.21561260.18862662X-RAY DIFFRACTION99
2.4358-2.51440.23171510.17722583X-RAY DIFFRACTION99
2.5144-2.60430.21211480.16892609X-RAY DIFFRACTION99
2.6043-2.70850.2171720.16572579X-RAY DIFFRACTION99
2.7085-2.83170.24121420.17452627X-RAY DIFFRACTION99
2.8317-2.98090.19691150.17192678X-RAY DIFFRACTION99
2.9809-3.16760.18881310.16892671X-RAY DIFFRACTION100
3.1676-3.4120.2011480.15772650X-RAY DIFFRACTION100
3.412-3.7550.20411260.14842675X-RAY DIFFRACTION100
3.755-4.29750.16511150.12762740X-RAY DIFFRACTION100
4.2975-5.41130.14221570.12212711X-RAY DIFFRACTION100
5.4113-35.37250.17691570.16172834X-RAY DIFFRACTION99
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)
17.14244.3769-3.65745.0195-3.34573.7157-0.1244-0.214-0.2466-0.1118-0.1326-0.42430.17990.2090.27820.18370.02350.02120.1021-0.09520.143236.91950.828544.1652
26.9751-0.04-1.13944.396-0.86367.242-0.20531.12620.4761-1.0334-0.009-0.3966-0.4538-0.15650.22440.4405-0.01060.01950.33310.02960.226923.16938.453933.1481
32.11870.1262-0.93791.2986-0.20791.69720.02760.01930.2384-0.04850.0213-0.0172-0.2174-0.0288-0.07220.23770.00170.01240.1794-0.0080.204628.01545.859140.852
45.1719-1.38391.67643.72380.1283.28760.04630.5025-0.2554-0.35920.0061-0.10690.37480.2438-0.050.37660.03920.05520.2317-0.02350.170334.1283-15.501329.4354
53.88261.2862.53494.31720.30763.1170.1042-0.0118-0.0514-0.1438-0.0120.20110.2162-0.2271-0.10170.19940.0170.05140.1774-0.00080.148425.486-9.219639.8719
66.80290.8073-5.50661.6762-2.1625.9406-0.47410.23511.0102-0.45390.44320.5563-1.1091-0.4931-0.12230.5030.0235-0.22150.27450.00420.400816.9335.650831.353
76.0304-2.8795-0.86224.55121.43622.3226-0.0956-0.01460.2345-0.1894-0.05830.66070.0575-0.31080.09040.1786-0.0277-0.0880.21140.08650.3908-0.7664.0434-9.9259
84.8846-2.0419-1.64713.34991.32923.7998-0.1302-0.47630.27110.29380.2321-0.0169-0.08450.2019-0.20730.1779-0.0013-0.04120.28760.04460.202312.70158.5277-0.5468
95.220.4575-2.29661.8248-0.10723.1183-0.0413-0.1590.161-0.09080.0490.2990.0178-0.0756-0.03250.14550.0118-0.04590.20490.0460.21386.77286.5705-8.3335
102.64260.3333-0.5283.93660.02854.9399-0.0016-0.4258-0.51170.42520.10640.53360.679-0.3579-0.03830.3324-0.05480.01390.28410.10610.34753.1571-10.93450.9751
115.60562.58373.09524.04295.65268.1264-0.0056-0.22170.44530.62990.0352-0.15280.04450.2665-0.05970.2580.0089-0.07030.2660.01830.238919.58336.98524.8515
120.66170.01061.78381.59840.0645.0805-0.17480.22370.3690.08180.05910.4057-0.2965-0.03750.09880.20890.0457-0.00350.26780.01140.27716.5927-0.572517.7519
130.8405-0.31391.96282.0539-0.28124.405-0.2139-0.00210.14330.11460.1785-0.0753-0.2944-0.0858-0.00610.21570.00020.00390.31090.02340.26715.3253-0.419815.6756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 71 )
3X-RAY DIFFRACTION3chain 'A' and (resid 72 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 206 )
5X-RAY DIFFRACTION5chain 'A' and (resid 207 through 233 )
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 248 )
7X-RAY DIFFRACTION7chain 'B' and (resid 6 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 95 )
9X-RAY DIFFRACTION9chain 'B' and (resid 96 through 154 )
10X-RAY DIFFRACTION10chain 'B' and (resid 155 through 233 )
11X-RAY DIFFRACTION11chain 'B' and (resid 234 through 251 )
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 23 )
13X-RAY DIFFRACTION13chain 'D' and (resid 9 through 23 )

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