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- PDB-6bch: I-LtrI E29D bound to cognate substrate (nicked complex) -

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Basic information

Entry
Database: PDB / ID: 6bch
TitleI-LtrI E29D bound to cognate substrate (nicked complex)
Components
  • DNA (26-MER)
  • DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
  • DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')
  • Ribosomal protein 3/homing endonuclease-like fusion protein
KeywordsHYDROLASE/DNA / Nucleid 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: 3 Å
AuthorsBrown, C. / Zhang, K. / McMurrough, T.A. / Gloor, G.B. / Edgell, D.R. / Junop, M.
CitationJournal: To Be Published
Title: I-LtrI E29D bound to cognate substrate (nicked complex)
Authors: 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
C: DNA (26-MER)
X: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')
D: Ribosomal protein 3/homing endonuclease-like fusion protein
E: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
F: DNA (26-MER)
G: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')
H: Ribosomal protein 3/homing endonuclease-like fusion protein
I: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
J: DNA (26-MER)
K: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')
L: Ribosomal protein 3/homing endonuclease-like fusion protein
N: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
O: DNA (26-MER)
P: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)208,93516
Polymers208,93516
Non-polymers00
Water18010
1
A: Ribosomal protein 3/homing endonuclease-like fusion protein
B: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
C: DNA (26-MER)
X: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,2344
Polymers52,2344
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-42 kcal/mol
Surface area18390 Å2
MethodPISA
2
D: Ribosomal protein 3/homing endonuclease-like fusion protein
E: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
F: DNA (26-MER)
G: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,2344
Polymers52,2344
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-42 kcal/mol
Surface area18510 Å2
MethodPISA
3
H: Ribosomal protein 3/homing endonuclease-like fusion protein
I: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
J: DNA (26-MER)
K: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,2344
Polymers52,2344
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7860 Å2
ΔGint-44 kcal/mol
Surface area18520 Å2
MethodPISA
4
L: Ribosomal protein 3/homing endonuclease-like fusion protein
N: DNA (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')
O: DNA (26-MER)
P: DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)52,2344
Polymers52,2344
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8000 Å2
ΔGint-43 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.760, 66.315, 169.924
Angle α, β, γ (deg.)90.03, 90.03, 90.22
Int Tables number1
Space group name H-MP1

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Components

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


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 (5'-D(*GP*GP*TP*CP*TP*AP*AP*AP*CP*GP*TP*CP*GP*TP*AP*T)-3')


Mass: 4913.203 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: DNA chain
DNA (5'-D(*TP*AP*GP*GP*AP*GP*CP*AP*TP*TP*T)-3')


Mass: 3388.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Leptographium truncatum (fungus)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.36 Å3/Da / Density % sol: 47.88 %
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: Dec 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3→66.21 Å / Num. obs: 14038 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 6.1
Reflection shellResolution: 3→3.0492 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3→38.913 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 38.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3065 1850 5 %
Rwork0.2543 --
obs0.257 14038 77.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→38.913 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8593 4252 0 10 12855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613501
X-RAY DIFFRACTIONf_angle_d1.00519251
X-RAY DIFFRACTIONf_dihedral_angle_d22.9545003
X-RAY DIFFRACTIONf_chiral_restr0.0432280
X-RAY DIFFRACTIONf_plane_restr0.0071718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.04920.39651400.3632756X-RAY DIFFRACTION77
3.0492-3.10170.50631760.35652568X-RAY DIFFRACTION76
3.1017-3.15810.46841070.36872683X-RAY DIFFRACTION75
3.1581-3.21880.52531220.30382302X-RAY DIFFRACTION70
3.2188-3.28450.34661660.29742348X-RAY DIFFRACTION69
3.2845-3.35590.50521020.28592505X-RAY DIFFRACTION70
3.3559-3.43390.37171940.28752551X-RAY DIFFRACTION76
3.4339-3.51970.53041100.28622637X-RAY DIFFRACTION77
3.5197-3.61480.35481010.29062569X-RAY DIFFRACTION71
3.6148-3.72110.28541550.27272445X-RAY DIFFRACTION73
3.7211-3.84110.38371290.29542828X-RAY DIFFRACTION81
3.8411-3.97830.38761650.29853029X-RAY DIFFRACTION85
3.9783-4.13740.36221420.2782855X-RAY DIFFRACTION84
4.1374-4.32540.27841250.24732951X-RAY DIFFRACTION85
4.3254-4.55320.27341420.24522877X-RAY DIFFRACTION84
4.5532-4.83790.3152120.23412840X-RAY DIFFRACTION82
4.8379-5.21070.27741590.2282769X-RAY DIFFRACTION80
5.2107-5.73360.29761340.2382617X-RAY DIFFRACTION77
5.7336-6.55980.26291010.25022551X-RAY DIFFRACTION72
6.5598-8.25170.21471170.22422776X-RAY DIFFRACTION80
8.2517-38.91580.16761850.18383219X-RAY DIFFRACTION93

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