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- PDB-6bdb: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bdb
TitleI-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex)
Components
  • (DNA (26-MER)) x 2
  • Ribosomal protein 3/homing endonuclease-like protein fusion
KeywordsHYDROLASE / Nucleic Acid
Function / homology
Function and homology information


endonuclease activity / ribosome / mitochondrion / metal ion binding
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: 1.5 Å
AuthorsBrown, C. / Zhang, K. / McMurrough, T.A. / Laforet, M. / Gloor, G.B. / Edgell, D.R. / Junop, M.
CitationJournal: To Be Published
Title: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex)
Authors: Laforet, M. / McMurrough, T.A. / Brown, C. / Junop, M. / Zhang, K. / Gloor, G.B.
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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: DNA (26-MER)
C: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)51,1103
Polymers51,1103
Non-polymers00
Water10,503583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8390 Å2
ΔGint-49 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.370, 67.190, 169.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35136.762 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
#2: DNA chain DNA (26-MER)


Mass: 7775.014 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#3: DNA chain DNA (26-MER)


Mass: 8198.330 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M DiAmmonium Phosphate 20% W/V PEG 3350

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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: 1.5→66.74 Å / Num. obs: 80496 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.056 / Net I/σ(I): 8.8
Reflection shellResolution: 1.5→1.517 Å / Rpim(I) all: 0.327

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.5→42.019 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2063 4055 5.04 %
Rwork0.1852 --
obs0.1863 80414 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→42.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 1060 0 583 3974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123575
X-RAY DIFFRACTIONf_angle_d1.3615055
X-RAY DIFFRACTIONf_dihedral_angle_d21.9961377
X-RAY DIFFRACTIONf_chiral_restr0.055576
X-RAY DIFFRACTIONf_plane_restr0.009455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.51770.27921220.2832566X-RAY DIFFRACTION100
1.5177-1.53620.27231310.2692634X-RAY DIFFRACTION100
1.5362-1.55560.28921520.26192577X-RAY DIFFRACTION100
1.5556-1.57610.27541250.24752608X-RAY DIFFRACTION100
1.5761-1.59770.26281460.23362605X-RAY DIFFRACTION100
1.5977-1.62050.28051180.23452595X-RAY DIFFRACTION100
1.6205-1.64470.23181240.22072629X-RAY DIFFRACTION100
1.6447-1.67040.2331290.22422639X-RAY DIFFRACTION100
1.6704-1.69780.2231220.21112578X-RAY DIFFRACTION100
1.6978-1.72710.25461350.21522623X-RAY DIFFRACTION100
1.7271-1.75850.25671570.20612556X-RAY DIFFRACTION100
1.7585-1.79230.20491290.21312636X-RAY DIFFRACTION100
1.7923-1.82890.26511420.20522615X-RAY DIFFRACTION100
1.8289-1.86860.24011270.20822627X-RAY DIFFRACTION100
1.8686-1.91210.22381390.20512603X-RAY DIFFRACTION100
1.9121-1.95990.21591420.20382627X-RAY DIFFRACTION100
1.9599-2.01290.22581510.19782589X-RAY DIFFRACTION100
2.0129-2.07220.21621600.19772628X-RAY DIFFRACTION100
2.0722-2.1390.19361310.19172601X-RAY DIFFRACTION100
2.139-2.21550.22471540.19462630X-RAY DIFFRACTION100
2.2155-2.30420.20351610.1912615X-RAY DIFFRACTION100
2.3042-2.4090.22941480.19492661X-RAY DIFFRACTION100
2.409-2.5360.21291450.19822615X-RAY DIFFRACTION100
2.536-2.69490.21211240.19382679X-RAY DIFFRACTION100
2.6949-2.90290.22351630.1912642X-RAY DIFFRACTION100
2.9029-3.1950.1961480.18652673X-RAY DIFFRACTION100
3.195-3.65710.18131400.16022701X-RAY DIFFRACTION100
3.6571-4.60660.15671550.14372708X-RAY DIFFRACTION100
4.6066-42.03590.17541350.14892899X-RAY DIFFRACTION100

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