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- PDB-6bce: Wild-type I-LtrI bound to cognate substrate (pre-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bce
TitleWild-type I-LtrI bound to cognate substrate (pre-cleavage complex)
Components
  • (DNA (27-MER)) x 2
  • Ribosomal protein 3/homing endonuclease-like fusion protein
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 (27-MER)
C: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7276
Polymers52,6073
Non-polymers1203
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8990 Å2
ΔGint-84 kcal/mol
Surface area17930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.261, 42.752, 103.380
Angle α, β, γ (deg.)90.00, 109.22, 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


Mass: 36015.234 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 (27-MER)


Mass: 8371.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#3: DNA chain DNA (27-MER)


Mass: 8220.325 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.14 M CHES pH 9.5 0.2M NaCl 10% W/V PEG 8000

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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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.75→56.02 Å / Num. obs: 48184 / % possible obs: 99.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 8
Reflection shellResolution: 1.75→1.7858 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3r7p

3r7p


Resolution: 1.75→38.503 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2252 2370 4.92 %
Rwork0.2011 --
obs0.2023 48154 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→38.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 1101 3 278 3653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093544
X-RAY DIFFRACTIONf_angle_d1.1365027
X-RAY DIFFRACTIONf_dihedral_angle_d22.7841376
X-RAY DIFFRACTIONf_chiral_restr0.057580
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78580.31311290.29532673X-RAY DIFFRACTION99
1.7858-1.82460.3221430.28352628X-RAY DIFFRACTION99
1.8246-1.8670.29121320.2742731X-RAY DIFFRACTION99
1.867-1.91370.3031250.25762653X-RAY DIFFRACTION99
1.9137-1.96550.31261310.25012662X-RAY DIFFRACTION99
1.9655-2.02330.30361380.24172675X-RAY DIFFRACTION99
2.0233-2.08860.2331350.23032674X-RAY DIFFRACTION100
2.0886-2.16320.28741440.22412683X-RAY DIFFRACTION100
2.1632-2.24980.24251560.21522695X-RAY DIFFRACTION100
2.2498-2.35220.2531670.21922664X-RAY DIFFRACTION100
2.3522-2.47620.2751420.22812691X-RAY DIFFRACTION100
2.4762-2.63130.25831290.22622704X-RAY DIFFRACTION100
2.6313-2.83440.25731360.21312702X-RAY DIFFRACTION100
2.8344-3.11960.22611340.21092712X-RAY DIFFRACTION99
3.1196-3.57070.1941530.17322688X-RAY DIFFRACTION99
3.5707-4.49760.1691350.16062720X-RAY DIFFRACTION99
4.4976-38.51270.19121410.1782829X-RAY DIFFRACTION100

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