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- PDB-6bda: Wild-type I-OnuI bound to A3G substrate (post-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bda
TitleWild-type I-OnuI bound to A3G substrate (post-cleavage complex)
Components
  • (Cleaved cognate DNA strand, -11 ...) x 2
  • Cleaved Cognate DNA strand, +11 sense
  • Cleaved cognate DNA strand, +11 antisense
  • Ribosomal protein 3/homing endonuclease-like protein fusionRibosome
KeywordsHYDROLASE/DNA / Nucleic Acid / HYDROLASE / HYDROLASE-DNA complex
Function / homology
Function and homology information


endonuclease activity / ribosome / mitochondrion
Similarity search - Function
LAGLIDADG endonuclease / Homing endonucleases / Endonuclease I-creI / Homing endonuclease, LAGLIDADG / Homing endonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Ribosomal protein 3/homing endonuclease-like protein fusion
Similarity search - Component
Biological speciesOphiostoma novo-ulmi subsp. americana (fungus)
Ophiostoma novo-ulmi (Dutch elm disease fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.88 Å
AuthorsBrown, C. / Zhang, K. / Laforet, M. / McMurrough, T. / Gloor, G.B. / Edgell, D.R. / Junop, M.
CitationJournal: To Be Published
Title: Wild-type I-OnuI bound to A3G substrate (post-cleavage complex)
Authors: Laforet, M. / McMurrough, T. / Brown, C. / Zhang, K. / Junop, M. / Gloor, G.B. / Edgell, D.R.
History
DepositionOct 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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.ptnr2_auth_asym_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_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: Ribosomal protein 3/homing endonuclease-like protein fusion
B: Cleaved Cognate DNA strand, +11 sense
C: Cleaved cognate DNA strand, -11 sense
D: Cleaved cognate DNA strand, -11 antisense
E: Cleaved cognate DNA strand, +11 antisense
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,60411
Polymers50,4585
Non-polymers1466
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-116 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.690, 68.980, 161.720
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 , 1 types, 1 molecules A

#1: Protein Ribosomal protein 3/homing endonuclease-like protein fusion / Ribosome


Mass: 35192.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiostoma novo-ulmi subsp. americana (fungus)
Gene: HEG fusion, rps3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VWW5

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DNA chain , 2 types, 2 molecules BE

#2: DNA chain Cleaved Cognate DNA strand, +11 sense


Mass: 4156.714 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#5: DNA chain Cleaved cognate DNA strand, +11 antisense


Mass: 3142.092 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)

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Cleaved cognate DNA strand, -11 ... , 2 types, 2 molecules CD

#3: DNA chain Cleaved cognate DNA strand, -11 sense


Mass: 3284.160 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#4: DNA chain Cleaved cognate DNA strand, -11 antisense


Mass: 4682.073 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)

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Non-polymers , 2 types, 476 molecules

#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Potassium Formate 20% W/V PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.88→68.98 Å / Num. obs: 39882 / % possible obs: 100 % / Redundancy: 5.8 % / Net I/σ(I): 7.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.88→41.276 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.68
RfactorNum. reflection% reflection
Rfree0.2326 1978 4.98 %
Rwork0.1911 --
obs0.1931 39721 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→41.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 1021 6 470 3864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063554
X-RAY DIFFRACTIONf_angle_d0.815003
X-RAY DIFFRACTIONf_dihedral_angle_d21.5511382
X-RAY DIFFRACTIONf_chiral_restr0.032566
X-RAY DIFFRACTIONf_plane_restr0.003454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.9270.28541380.28312652X-RAY DIFFRACTION100
1.927-1.97910.32181440.26742635X-RAY DIFFRACTION100
1.9791-2.03740.29021430.24722661X-RAY DIFFRACTION100
2.0374-2.10310.28441400.24422630X-RAY DIFFRACTION100
2.1031-2.17830.24611330.21762667X-RAY DIFFRACTION100
2.1783-2.26550.2441420.2142674X-RAY DIFFRACTION100
2.2655-2.36860.26261380.21432671X-RAY DIFFRACTION100
2.3686-2.49340.25591540.2122660X-RAY DIFFRACTION100
2.4934-2.64960.26521260.21242700X-RAY DIFFRACTION100
2.6496-2.85420.28091460.21872693X-RAY DIFFRACTION100
2.8542-3.14130.25191400.20642725X-RAY DIFFRACTION100
3.1413-3.59560.15711360.17162701X-RAY DIFFRACTION99
3.5956-4.52920.21171380.15092779X-RAY DIFFRACTION100
4.5292-41.28610.20691600.14892895X-RAY DIFFRACTION100

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