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- PDB-6bd0: I-OnuI K227Y, D236A bound to cognate substrate (pre-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bd0
TitleI-OnuI K227Y, D236A bound to cognate substrate (pre-cleavage complex)
Components
  • (DNA (25-MER)) x 2
  • Ribosomal protein 3/homing endonuclease-like protein fusion
KeywordsHYDROLASE/DNA / Nucleic Acid / HYDROLASE / HYDROLASE-DNA complex
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: 1.45 Å
AuthorsBrown, C. / Zhang, K. / Laforet, M. / McMurrough, T.A. / Gloor, G.B. / Edgell, D.R. / Junop, M.
CitationJournal: To Be Published
Title: I-OnuI K227Y, D236A bound to cognate substrate (pre-cleavage complex)
Authors: Laforet, M. / McMurrough, T.A. / Brown, C. / Zhang, K. / Junop, M. / Gloor, G.B. / Edgell, D.R.
History
DepositionOct 20, 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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: Ribosomal protein 3/homing endonuclease-like protein fusion
B: DNA (25-MER)
C: DNA (25-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9916
Polymers49,8713
Non-polymers1203
Water13,403744
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8960 Å2
ΔGint-89 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.880, 66.740, 159.830
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: 34517.066 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 (25-MER)


Mass: 7469.833 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#3: DNA chain DNA (25-MER)


Mass: 7884.135 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.24 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.18 M Tri-ammonium Citrate 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 PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.45→66.74 Å / Num. obs: 80496 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.046 / Net I/σ(I): 8.93
Reflection shellResolution: 1.45→1.46 Å / Rpim(I) all: 0.334

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.45→37.095 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.55
RfactorNum. reflection% reflection
Rfree0.1899 4108 5.12 %
Rwork0.1646 --
obs0.1659 80292 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→37.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 1019 3 744 4167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0193600
X-RAY DIFFRACTIONf_angle_d1.7965071
X-RAY DIFFRACTIONf_dihedral_angle_d21.71404
X-RAY DIFFRACTIONf_chiral_restr0.103573
X-RAY DIFFRACTIONf_plane_restr0.014463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.46710.30611120.272596X-RAY DIFFRACTION100
1.4671-1.4850.2881520.24982610X-RAY DIFFRACTION100
1.485-1.50380.27351540.23752566X-RAY DIFFRACTION100
1.5038-1.52350.23491390.21992538X-RAY DIFFRACTION100
1.5235-1.54440.24221300.21872636X-RAY DIFFRACTION100
1.5444-1.56650.23361290.20172556X-RAY DIFFRACTION100
1.5665-1.58990.23311510.1972621X-RAY DIFFRACTION100
1.5899-1.61470.21971480.19432590X-RAY DIFFRACTION100
1.6147-1.64120.24041510.18682563X-RAY DIFFRACTION100
1.6412-1.66950.19631260.18312645X-RAY DIFFRACTION100
1.6695-1.69980.22551510.17832571X-RAY DIFFRACTION100
1.6998-1.73250.22381360.16862596X-RAY DIFFRACTION100
1.7325-1.76790.19921320.16852608X-RAY DIFFRACTION100
1.7679-1.80630.20281580.16832586X-RAY DIFFRACTION100
1.8063-1.84830.19451410.16832603X-RAY DIFFRACTION100
1.8483-1.89460.20751300.16032637X-RAY DIFFRACTION100
1.8946-1.94580.19531400.16472597X-RAY DIFFRACTION100
1.9458-2.0030.19771410.16292635X-RAY DIFFRACTION100
2.003-2.06770.19861530.16032603X-RAY DIFFRACTION100
2.0677-2.14160.19791500.15522625X-RAY DIFFRACTION100
2.1416-2.22730.20871380.1562647X-RAY DIFFRACTION100
2.2273-2.32870.16841490.16442636X-RAY DIFFRACTION100
2.3287-2.45140.20881360.16712631X-RAY DIFFRACTION100
2.4514-2.6050.17391330.16552651X-RAY DIFFRACTION100
2.605-2.8060.20041450.172682X-RAY DIFFRACTION100
2.806-3.08830.18851340.1722657X-RAY DIFFRACTION100
3.0883-3.53490.16081260.14442719X-RAY DIFFRACTION100
3.5349-4.45240.14131580.13332720X-RAY DIFFRACTION100
4.4524-37.1070.16971650.15292859X-RAY DIFFRACTION100

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