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

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Basic information

Entry
Database: PDB / ID: 6bcn
TitleI-LtrI E184D bound to cognate substrate (pre-cleavage complex)
Components
  • (DNA (26-MER)) x 2
  • 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
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: 2.5 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 2.0Oct 31, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Mar 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
C: Ribosomal protein 3/homing endonuclease-like fusion protein
G: Ribosomal protein 3/homing endonuclease-like fusion protein
J: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (26-MER)
D: DNA (26-MER)
E: DNA (26-MER)
F: DNA (26-MER)
H: DNA (26-MER)
I: DNA (26-MER)
K: DNA (26-MER)
L: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,57625
Polymers209,05512
Non-polymers52113
Water3,405189
1
A: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (26-MER)
D: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4247
Polymers52,2643
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-97 kcal/mol
Surface area17900 Å2
MethodPISA
2
C: Ribosomal protein 3/homing endonuclease-like fusion protein
E: DNA (26-MER)
F: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4247
Polymers52,2643
Non-polymers1604
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9030 Å2
ΔGint-94 kcal/mol
Surface area17630 Å2
MethodPISA
3
G: Ribosomal protein 3/homing endonuclease-like fusion protein
H: DNA (26-MER)
I: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3445
Polymers52,2643
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-72 kcal/mol
Surface area17630 Å2
MethodPISA
4
J: Ribosomal protein 3/homing endonuclease-like fusion protein
K: DNA (26-MER)
L: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3846
Polymers52,2643
Non-polymers1203
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8660 Å2
ΔGint-86 kcal/mol
Surface area17800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.650, 64.020, 168.976
Angle α, β, γ (deg.)89.93, 90.19, 93.64
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36001.211 Da / Num. of mol.: 4
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: 8042.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#3: DNA chain
DNA (26-MER)


Mass: 8220.325 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M TRIS pH7.0 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 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: 2.5→84.49 Å / Num. obs: 60488 / % possible obs: 98 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 3.9
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.7 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.5→35.71 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 34.58
RfactorNum. reflection% reflection
Rfree0.2762 3106 5.34 %
Rwork0.2372 --
obs0.2393 58163 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9054 4235 13 189 13491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713953
X-RAY DIFFRACTIONf_angle_d1.57919779
X-RAY DIFFRACTIONf_dihedral_angle_d22.9345366
X-RAY DIFFRACTIONf_chiral_restr0.0792286
X-RAY DIFFRACTIONf_plane_restr0.0051786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53910.44121410.39532312X-RAY DIFFRACTION89
2.5391-2.58070.39151660.37342341X-RAY DIFFRACTION89
2.5807-2.62520.46031440.36842386X-RAY DIFFRACTION90
2.6252-2.67290.37911620.36822386X-RAY DIFFRACTION89
2.6729-2.72430.41471560.33532317X-RAY DIFFRACTION90
2.7243-2.77990.38441210.34152460X-RAY DIFFRACTION91
2.7799-2.84030.40441140.32182475X-RAY DIFFRACTION92
2.8403-2.90630.42161280.32472467X-RAY DIFFRACTION93
2.9063-2.9790.32661030.30592505X-RAY DIFFRACTION94
2.979-3.05950.36371500.30062572X-RAY DIFFRACTION94
3.0595-3.14940.35561450.27932437X-RAY DIFFRACTION94
3.1494-3.2510.3151560.26212523X-RAY DIFFRACTION94
3.251-3.36710.32371200.24152484X-RAY DIFFRACTION93
3.3671-3.50180.25231270.22542530X-RAY DIFFRACTION95
3.5018-3.66110.26081300.21992586X-RAY DIFFRACTION97
3.6611-3.85390.25681450.21622615X-RAY DIFFRACTION98
3.8539-4.0950.20221750.19932528X-RAY DIFFRACTION98
4.095-4.41070.22171390.17622658X-RAY DIFFRACTION98
4.4107-4.85350.21561670.17962579X-RAY DIFFRACTION99
4.8535-5.55360.19651260.19772641X-RAY DIFFRACTION99
5.5536-6.98840.22211340.19622655X-RAY DIFFRACTION99
6.9884-35.71360.19781570.1692600X-RAY DIFFRACTION98

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