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- PDB-6bct: I-LtrI E184D bound to non-cognate C4 substrate (pre-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bct
TitleI-LtrI E184D bound to non-cognate C4 substrate (pre-cleavage complex)
Components
  • DNA (26-MER)
  • DNA (27-MER)
  • Ribosomal protein 3/homing endonuclease-like fusion proteinRibosome
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 fusion protein
Similarity search - Component
Biological speciesLeptographium truncatum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.73 Å
AuthorsBrown, C. / Zhang, K. / McMurrough, T.A. / Gloor, G.B. / Edgell, D.R. / Junop, M.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Active site residue identity regulates cleavage preference of LAGLIDADG homing endonucleases.
Authors: McMurrough, T.A. / Brown, C.M. / Zhang, K. / Hausner, G. / Junop, M.S. / 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 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 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_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 fusion protein
B: DNA (26-MER)
D: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4096
Polymers52,2893
Non-polymers1203
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-87 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.611, 43.440, 105.210
Angle α, β, γ (deg.)90.00, 106.95, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36001.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptographium truncatum (fungus) / Gene: HEG fusion, rps3 / Production host: Escherichia coli (E. coli) / References: UniProt: C7SWF3
#2: DNA chain DNA (26-MER)


Mass: 8058.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#3: DNA chain DNA (27-MER)


Mass: 8229.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M TRIS pH 7.0 20% W/V PEG 2000 MME

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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: 2.73→56.22 Å / Num. obs: 13720 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.6
Reflection shellResolution: 2.73→2.86 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.73→33.547 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.94
RfactorNum. reflection% reflection
Rfree0.2816 665 4.9 %
Rwork0.227 --
obs0.2296 13576 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.73→33.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 1084 3 0 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043444
X-RAY DIFFRACTIONf_angle_d0.694898
X-RAY DIFFRACTIONf_dihedral_angle_d22.331286
X-RAY DIFFRACTIONf_chiral_restr0.033576
X-RAY DIFFRACTIONf_plane_restr0.002440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7301-2.94080.44851260.33292552X-RAY DIFFRACTION99
2.9408-3.23650.36051260.29952552X-RAY DIFFRACTION98
3.2365-3.70430.36811200.26192526X-RAY DIFFRACTION98
3.7043-4.6650.27381380.2162603X-RAY DIFFRACTION100
4.665-33.54910.22391550.18842678X-RAY DIFFRACTION100

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