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- PDB-6ozi: Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234... -

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Basic information

Entry
Database: PDB / ID: 6ozi
TitleCrystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine
Components
  • DNA/RNA (23-MER)
  • endonuclease V isoform X2
KeywordsHYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination
Function / homology
Function and homology information


endonuclease activity / DNA repair
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 isoform X2
Similarity search - Component
Biological speciesCiona intestinalis (vase tunicate)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 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 / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: endonuclease V isoform X2
B: endonuclease V isoform X2
C: DNA/RNA (23-MER)
D: DNA/RNA (23-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,73610
Polymers69,2794
Non-polymers4576
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8550 Å2
ΔGint-41 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.079, 81.428, 166.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 5:15 or resseq 17:21 or resseq...
21(chain B and (resseq 5:15 or resseq 17:21 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 5:15 or resseq 17:21 or resseq...A5 - 15
121(chain A and (resseq 5:15 or resseq 17:21 or resseq...A17 - 21
131(chain A and (resseq 5:15 or resseq 17:21 or resseq...A23 - 26
141(chain A and (resseq 5:15 or resseq 17:21 or resseq...A28 - 33
151(chain A and (resseq 5:15 or resseq 17:21 or resseq...A2 - 38
161(chain A and (resseq 5:15 or resseq 17:21 or resseq...A40 - 42
171(chain A and (resseq 5:15 or resseq 17:21 or resseq...A44 - 45
181(chain A and (resseq 5:15 or resseq 17:21 or resseq...A47 - 49
191(chain A and (resseq 5:15 or resseq 17:21 or resseq...A2 - 245
1101(chain A and (resseq 5:15 or resseq 17:21 or resseq...A2 - 245
1111(chain A and (resseq 5:15 or resseq 17:21 or resseq...A138
1121(chain A and (resseq 5:15 or resseq 17:21 or resseq...A2 - 245
1131(chain A and (resseq 5:15 or resseq 17:21 or resseq...A171 - 208
1141(chain A and (resseq 5:15 or resseq 17:21 or resseq...A210 - 244
211(chain B and (resseq 5:15 or resseq 17:21 or resseq...B5 - 15
221(chain B and (resseq 5:15 or resseq 17:21 or resseq...B17 - 21
231(chain B and (resseq 5:15 or resseq 17:21 or resseq...B23 - 26
241(chain B and (resseq 5:15 or resseq 17:21 or resseq...B5 - 42
251(chain B and (resseq 5:15 or resseq 17:21 or resseq...B0
261(chain B and (resseq 5:15 or resseq 17:21 or resseq...B40 - 42
271(chain B and (resseq 5:15 or resseq 17:21 or resseq...B44 - 45
281(chain B and (resseq 5:15 or resseq 17:21 or resseq...B47 - 49
291(chain B and (resseq 5:15 or resseq 17:21 or resseq...B5 - 245
2101(chain B and (resseq 5:15 or resseq 17:21 or resseq...B5 - 245
2111(chain B and (resseq 5:15 or resseq 17:21 or resseq...B138
2121(chain B and (resseq 5:15 or resseq 17:21 or resseq...B171 - 208
2131(chain B and (resseq 5:15 or resseq 17:21 or resseq...B210 - 244

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Components

#1: Protein endonuclease V isoform X2


Mass: 27612.131 Da / Num. of mol.: 2 / Mutation: D234N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ciona intestinalis (vase tunicate) / Gene: LOC100181026 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3Q0JV13
#2: DNA/RNA hybrid DNA/RNA (23-MER)


Mass: 7027.521 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.6 Å3/Da / Density % sol: 52.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium fluoride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Apr 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 29100 / % possible obs: 92.3 % / Redundancy: 1 % / Biso Wilson estimate: 30.12 Å2 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsDiffraction-ID% possible all
2.3-2.3912347172.7
2.3-2.341631194.2

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→30 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.53
RfactorNum. reflection% reflection
Rfree0.201 1468 5.05 %
Rwork0.1743 --
obs0.1757 29058 92.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103.37 Å2 / Biso mean: 36.9597 Å2 / Biso min: 17.18 Å2
Refinement stepCycle: final / Resolution: 2.302→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3849 753 24 439 5065
Biso mean--46.6 36.78 -
Num. residues----522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054842
X-RAY DIFFRACTIONf_angle_d0.7756684
X-RAY DIFFRACTIONf_chiral_restr0.048758
X-RAY DIFFRACTIONf_plane_restr0.005716
X-RAY DIFFRACTIONf_dihedral_angle_d14.432875
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2101X-RAY DIFFRACTION8.394TORSIONAL
12B2101X-RAY DIFFRACTION8.394TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3018-2.38410.23541200.2012114223472
2.3841-2.47950.21481100.20792406251681
2.4795-2.59230.24431470.21112533268087
2.5923-2.72880.23061320.21812700283291
2.7288-2.89970.26371620.21672856301896
2.8997-3.12340.23781540.20632891304598
3.1234-3.43730.21771610.18042969313099
3.4373-3.93370.20961570.167329973154100
3.9337-4.95240.16711460.134930233169100
4.9524-29.95690.1441790.14713101328097
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)
17.4951-4.7109-4.69829.31135.03356.72110.06121.1740.0521-0.5896-0.6379-0.1364-0.2158-0.41390.48810.2561-0.07170.01160.46050.09870.2875-4.876542.9947-28.1191
22.76881.47960.96622.25571.28893.6562-0.0395-0.19820.39470.1344-0.09760.1373-0.1703-0.10350.13520.16070.0264-0.03180.18790.00620.2613-25.21539.0956-14.5919
32.83260.00391.77024.174-0.38082.56670.380.4694-0.1417-0.7095-0.0189-0.4191-0.00850.6874-0.20580.17920.039-0.01840.3257-0.06190.2517-20.384225.8758-30.1755
42.26470.34140.68431.01220.57581.8253-0.05460.14670.2205-0.1732-0.01650.0809-0.0737-0.0270.07260.13950.0142-0.00830.1610.02020.1744-18.934535.9697-21.5815
55.35380.987-0.45756.2694-1.11515.22850.0987-0.0485-0.33540.1447-0.0677-0.39150.16940.28340.03190.14880.0087-0.01250.158-0.03590.1585-7.542332.0833-1.4788
63.45120.9704-0.43277.7716-1.33813.89330.0929-0.24280.01280.285-0.0480.07630.1972-0.2113-0.08980.1066-0.0201-0.04650.1975-0.0130.1222-20.277230.8433-7.5675
75.8648-2.7085-5.00016.68776.38298.8137-0.02880.2315-0.1572-0.1974-0.23390.07440.2968-0.12310.14780.24280.0331-0.03980.23080.02790.1773-24.180221.4813-25.7782
86.713-4.4375-2.8166.50910.33028.28870.18740.7677-0.6364-0.4557-0.00641.37550.3334-1.3858-0.1380.334-0.0772-0.11510.4920.04430.6326-35.1029-19.761-25.009
91.34830.70481.23517.1089-3.75954.1942-0.008-0.0072-0.29530.0791-0.0916-0.22040.19420.25120.12390.2180.0129-0.04430.2026-0.04470.1757-12.3224-14.3722-30.1307
103.38480.1401-1.28375.8540.38955.8919-0.198-0.13860.3442-0.08410.1181.3316-0.3069-1.18420.14760.2860.0793-0.08290.46240.00340.4796-25.17411.3166-32.0298
111.06360.0591-0.68412.2336-1.46673.97030.00190.27720.0323-0.04810.17940.28520.0109-0.4115-0.24810.33540.0176-0.09880.1937-0.00080.276-22.2547-6.4245-33.8418
121.34490.4807-0.41891.9757-0.68650.95680.0446-0.16920.00960.4818-0.0544-0.0484-0.04560.0439-0.00520.39050.0297-0.10250.21020.02450.269-15.1573-12.9369-18.1597
135.3676-4.99476.59444.9158-6.30068.2249-0.443-0.26970.48970.5150.2786-0.2067-0.8074-0.53990.26870.430.066-0.09010.2403-0.00990.3143-18.93895.3423-31.03
148.0858-2.8674-4.38113.06760.85434.0285-0.25610.0398-0.22170.13960.0313-0.5732-0.10160.59630.19870.1496-0.01180.0030.3404-0.04510.3189-0.09627.547-20.0759
153.0645-1.94331.64082.9567-4.06376.26780.3899-0.0545-0.5219-0.8623-0.26850.47990.91330.1904-0.07260.382-0.0026-0.09190.2364-0.00340.3293-11.494115.451-23.471
166.3186-1.70270.87094.88661.71953.8165-0.5032-0.6045-0.3813-0.11410.29110.89850.6584-0.90170.16840.4758-0.101-0.0330.50150.1370.5209-21.34894.9439-11.5276
176.8941-4.7118-1.94548.87922.9711.629-0.2739-0.51170.1158-0.8954-0.13291.1258-0.33780.67620.27060.6196-0.0216-0.13380.29030.02110.431-26.2843-1.1585-19.0714
185.4085-3.5881-4.12965.77041.11654.31480.1368-0.69290.002-0.63330.10660.0856-0.0690.1452-0.18890.4772-0.067-0.0550.2534-0.01620.29-17.512414.3366-12.316
196.37893.1413-4.2058.1153-4.11246.7884-0.0747-0.1023-0.21540.1045-0.1566-0.78450.42920.8110.05220.2524-0.00660.00710.3959-0.02730.4606-2.613220.0297-22.8801
202.199-2.3129-0.91163.14150.10335.834-0.20870.42221.4367-0.3485-0.0796-0.2407-0.6202-0.80560.32440.2180.04160.0510.53170.02270.70365.004633.177-26.9641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 23 )A2 - 23
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 46 )A24 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 62 )A47 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 157 )A63 - 157
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 191 )A158 - 191
6X-RAY DIFFRACTION6chain 'A' and (resid 192 through 227 )A192 - 227
7X-RAY DIFFRACTION7chain 'A' and (resid 228 through 245 )A228 - 245
8X-RAY DIFFRACTION8chain 'B' and (resid 5 through 23 )B5 - 23
9X-RAY DIFFRACTION9chain 'B' and (resid 24 through 46 )B24 - 46
10X-RAY DIFFRACTION10chain 'B' and (resid 47 through 62 )B47 - 62
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 105 )B63 - 105
12X-RAY DIFFRACTION12chain 'B' and (resid 106 through 227 )B106 - 227
13X-RAY DIFFRACTION13chain 'B' and (resid 228 through 245 )B228 - 245
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 6 )C1 - 6
15X-RAY DIFFRACTION15chain 'C' and (resid 7 through 11 )C7 - 11
16X-RAY DIFFRACTION16chain 'C' and (resid 12 through 17 )C12 - 17
17X-RAY DIFFRACTION17chain 'D' and (resid 4 through 9 )D4 - 9
18X-RAY DIFFRACTION18chain 'D' and (resid 10 through 14 )D10 - 14
19X-RAY DIFFRACTION19chain 'D' and (resid 15 through 19 )D15 - 19
20X-RAY DIFFRACTION20chain 'D' and (resid 20 through 23 )D20 - 23

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