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- PDB-6bcf: I-LtrI G183A bound to cognate substrate (pre-cleavage complex) -

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Basic information

Entry
Database: PDB / ID: 6bcf
TitleI-LtrI G183A bound to cognate substrate (pre-cleavage complex)
Components
  • (DNA (26-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: 2.92 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
D: Ribosomal protein 3/homing endonuclease-like fusion protein
E: DNA (26-MER)
F: DNA (26-MER)
A: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (26-MER)
C: DNA (26-MER)
G: Ribosomal protein 3/homing endonuclease-like fusion protein
H: DNA (26-MER)
I: DNA (26-MER)
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)208,49124
Polymers208,01012
Non-polymers48112
Water00
1
D: 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)52,1236
Polymers52,0033
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-89 kcal/mol
Surface area18290 Å2
MethodPISA
2
A: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (26-MER)
C: DNA (26-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1236
Polymers52,0033
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-91 kcal/mol
Surface area18180 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)52,1236
Polymers52,0033
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-89 kcal/mol
Surface area18160 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)52,1236
Polymers52,0033
Non-polymers1203
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-87 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.956, 66.770, 169.414
Angle α, β, γ (deg.)90.12, 90.08, 90.06
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 36029.262 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: 7931.144 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.: 12 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris pH 7.0 20% W/V PEG2000 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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.92→66.77 Å / Num. obs: 72648 / % possible obs: 98 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9201→2.9585 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 2 / Num. unique all: 4530 / % possible all: 96.9

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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: 2.92→38.992 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.63
RfactorNum. reflection% reflection
Rfree0.3086 2075 5.05 %
Rwork0.2391 --
obs0.2425 72648 86.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.92→38.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 4249 12 0 12768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113416
X-RAY DIFFRACTIONf_angle_d1.33719147
X-RAY DIFFRACTIONf_dihedral_angle_d23.0444972
X-RAY DIFFRACTIONf_chiral_restr0.0622286
X-RAY DIFFRACTIONf_plane_restr0.0081701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9201-2.95850.38381690.34222637X-RAY DIFFRACTION88
2.9585-2.9990.38371360.33282610X-RAY DIFFRACTION89
2.999-3.04180.55871780.33862707X-RAY DIFFRACTION88
3.0418-3.08720.39791460.33982630X-RAY DIFFRACTION85
3.0872-3.13540.35331840.34292617X-RAY DIFFRACTION85
3.1354-3.18680.42641460.3082569X-RAY DIFFRACTION86
3.1868-3.24170.40071700.25452362X-RAY DIFFRACTION80
3.2417-3.30070.2198960.26242443X-RAY DIFFRACTION79
3.3007-3.36410.4521160.2832590X-RAY DIFFRACTION80
3.3641-3.43270.32491120.27522501X-RAY DIFFRACTION84
3.4327-3.50730.38911430.2772620X-RAY DIFFRACTION87
3.5073-3.58890.351380.25092593X-RAY DIFFRACTION85
3.5889-3.67850.29181560.26712683X-RAY DIFFRACTION85
3.6785-3.77790.28661070.25972553X-RAY DIFFRACTION87
3.7779-3.8890.37371720.25112754X-RAY DIFFRACTION89
3.889-4.01440.3313860.26812909X-RAY DIFFRACTION91
4.0144-4.15770.34051500.24812692X-RAY DIFFRACTION91
4.1577-4.3240.28531530.23812735X-RAY DIFFRACTION91
4.324-4.52050.35771960.20852681X-RAY DIFFRACTION90
4.5205-4.75840.34391270.22332785X-RAY DIFFRACTION89
4.7584-5.0560.2786940.21232719X-RAY DIFFRACTION88
5.056-5.44540.39811530.22722646X-RAY DIFFRACTION87
5.4454-5.99160.21051230.19882519X-RAY DIFFRACTION84
5.9916-6.85460.25851570.20252720X-RAY DIFFRACTION89
6.8546-8.62060.2721340.21242814X-RAY DIFFRACTION90
8.6206-38.99550.1981300.19992887X-RAY DIFFRACTION94

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