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

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Basic information

Entry
Database: PDB / ID: 6ozm
TitleCrystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 10 min soak in 10 mM Mn2+
Components
  • DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
  • Endonuclease V
KeywordsHYDROLASE/RNA / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination / HYDROLASE-RNA complex
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 / 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_alt_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_seq_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_alt_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.pdbx_ptnr1_label_alt_id / _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

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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 (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
D: DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,72117
Polymers70,6844
Non-polymers1,03813
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-80 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.401, 72.322, 155.311
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 (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')


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

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Non-polymers , 5 types, 253 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsChains C and D are partially cleaved between residues 11 and 12. Conformation A represents the ...Chains C and D are partially cleaved between residues 11 and 12. Conformation A represents the substrate state. Conformation B represents the product state.

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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: 2.88 Å3/Da / Density % sol: 57.3 %
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: Jul 19, 2016
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: 42984 / % possible obs: 92.4 % / Redundancy: 5.2 % / Net I/σ(I): 18.6
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 1522

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→35.717 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.74
RfactorNum. reflection% reflection
Rfree0.2163 2259 5.27 %
Rwork0.1737 --
obs0.176 42885 91.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→35.717 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 632 55 240 4722
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084723
X-RAY DIFFRACTIONf_angle_d0.9916504
X-RAY DIFFRACTIONf_dihedral_angle_d15.8942784
X-RAY DIFFRACTIONf_chiral_restr0.054770
X-RAY DIFFRACTIONf_plane_restr0.006723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1325-2.17880.2925910.24281621X-RAY DIFFRACTION59
2.1788-2.22950.25331040.22931966X-RAY DIFFRACTION72
2.2295-2.28530.24911270.2192091X-RAY DIFFRACTION77
2.2853-2.3470.291430.2152192X-RAY DIFFRACTION81
2.347-2.41610.24891130.20442383X-RAY DIFFRACTION86
2.4161-2.49410.24011270.21092573X-RAY DIFFRACTION93
2.4941-2.58320.24221470.20422694X-RAY DIFFRACTION98
2.5832-2.68660.27851420.20172738X-RAY DIFFRACTION99
2.6866-2.80880.24791360.20492761X-RAY DIFFRACTION100
2.8088-2.95680.27871720.21112736X-RAY DIFFRACTION100
2.9568-3.1420.25681540.20582763X-RAY DIFFRACTION100
3.142-3.38440.20711540.19112746X-RAY DIFFRACTION99
3.3844-3.72470.22731700.16312777X-RAY DIFFRACTION100
3.7247-4.26290.17491820.13642784X-RAY DIFFRACTION100
4.2629-5.36780.16331110.1252886X-RAY DIFFRACTION100
5.3678-35.72180.18381860.16262915X-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)
17.79565.7539-4.68885.9759-4.22444.5907-0.0809-0.2604-0.42770.002-0.3226-0.40510.25970.18650.42070.33210.06440.01650.16-0.05470.144336.69710.912844.8433
25.8184-0.7116-0.17934.1155-0.78351.6426-0.10110.79120.6738-1.0034-0.00150.0353-0.1787-0.0710.09090.5578-0.0108-0.05470.42860.00040.212523.0939.597134.4555
32.31290.4366-0.40231.5994-0.40131.7679-0.0530.02370.2149-0.15060.01710.0391-0.1096-0.07210.01460.36530.0366-0.01090.21740.00190.147628.31926.430941.4492
41.5965-0.38020.30053.2418-0.20353.3073-0.02320.1694-0.0618-0.6412-0.01040.12010.3564-0.09670.05420.5701-0.0122-0.00320.25860.00670.167127.9904-7.895333.2435
58.2902-4.8687-2.98486.55623.46465.2486-0.1243-0.08260.08770.0597-0.16830.70720.1355-0.25030.35660.3365-0.0768-0.06030.2320.03370.32780.31452.9218-10.8307
64.6755-0.8136-0.78243.07531.05783.4227-0.1562-0.43050.51390.73610.153-0.1474-0.12130.2937-0.09360.5070.009-0.08750.308-0.01420.228412.9788.7605-1.0326
74.974-0.5058-4.77624.5790.1054.80750.2891-0.48411.110.27730.15970.1095-0.95760.328-0.4280.3785-0.0174-0.11030.3697-0.03730.314810.164313.0064-7.9261
83.0477-0.6015-0.23915.1178-0.35453.9131-0.1806-0.4855-0.38190.9240.13830.80460.574-0.3202-0.06180.5984-0.03420.09370.31620.0320.28972.2717-5.6559-1.2348
93.76760.97832.64862.98830.94835.0220.0166-0.150.06670.74-0.0238-0.12760.21540.2949-0.04890.4990.0307-0.04580.31460.02370.188513.3301-1.1348-0.6667
101.04560.17982.8163.890.03485.8384-0.46950.19750.3751-0.5863-0.04050.5857-0.3931-0.04850.43370.53490.0735-0.06420.3541-0.04070.339419.96820.321719.7166
112.2414-1.36414.06023.1544-1.72257.5364-0.1667-0.08410.17140.12960.0104-0.1494-0.5611-0.13110.10250.5486-0.03040.00520.37540.0070.261414.91780.612515.4382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 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 251 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 46 )
6X-RAY DIFFRACTION6chain 'B' and (resid 47 through 95 )
7X-RAY DIFFRACTION7chain 'B' and (resid 96 through 114 )
8X-RAY DIFFRACTION8chain 'B' and (resid 115 through 206 )
9X-RAY DIFFRACTION9chain 'B' and (resid 207 through 251 )
10X-RAY DIFFRACTION10chain 'C' and (resid 9 through 23 )
11X-RAY DIFFRACTION11chain 'D' and (resid 9 through 23 )

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