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- PDB-5e63: K262A mutant of I-SmaMI -

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Basic information

Entry
Database: PDB / ID: 5.0E+63
TitleK262A mutant of I-SmaMI
Components
  • DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')
  • DNA left half site bottom strand
  • DNA left site top strand
  • DNA right half site Bottom strand
  • I-SmaMI LAGLIDADG meganuclease
KeywordsHydrolase/DNA / LAGLIDADG / I-SmaMI / K262A / mutant / Hydrolase-DNA complex
Function / homology
Function and homology information


endonuclease activity / 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
2-METHOXYETHANOL / DNA / DNA (> 10) / Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShen, B. / Stoddard, B.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: The Structural Basis of Asymmetry in DNA Binding and Cleavage as Exhibited by the I-SmaMI LAGLIDADG Meganuclease.
Authors: Shen, B.W. / Lambert, A. / Walker, B.C. / Stoddard, B.L. / Kaiser, B.K.
History
DepositionOct 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Apr 6, 2016Group: Source and taxonomy
Revision 1.3Sep 27, 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_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: I-SmaMI LAGLIDADG meganuclease
B: DNA right half site Bottom strand
C: DNA left half site bottom strand
D: DNA left site top strand
E: DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,63110
Polymers49,3625
Non-polymers2695
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-81 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.835, 67.694, 97.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein I-SmaMI LAGLIDADG meganuclease


Mass: 34094.539 Da / Num. of mol.: 1 / Fragment: UNP residues 114-415 / Mutation: K262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria macrospora (strain ATCC MYA-333 / DSM 997 / K(L3346) / K-hell) (fungus)
Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Plasmid: pET21d(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F7WD42

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DNA chain , 4 types, 4 molecules BCDE

#2: DNA chain DNA right half site Bottom strand


Mass: 4248.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA left half site bottom strand


Mass: 3398.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA left site top strand


Mass: 4534.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: DNA chain DNA (5'-D(P*CP*AP*GP*GP*TP*GP*TP*AP*CP*G)-3')


Mass: 3085.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 54 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-MXE / 2-METHOXYETHANOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#8: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 38.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28-32% PEGMME550, HEPES Mg++ / PH range: 7.5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 70 / Detector: CCD / Date: Apr 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 12826 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7 % / Biso Wilson estimate: 26.8 Å2 / Rsym value: 0.132 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.661 / Mean I/σ(I) obs: 3.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LOX

4lox


Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.88 / SU B: 28.858 / SU ML: 0.292 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27861 618 4.9 %RANDOM
Rwork0.18861 ---
obs0.19296 12093 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.99 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 1021 16 49 3420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0173548
X-RAY DIFFRACTIONr_bond_other_d0.0030.022940
X-RAY DIFFRACTIONr_angle_refined_deg2.041.6934988
X-RAY DIFFRACTIONr_angle_other_deg1.30536826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8885292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91724.38898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.8615445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.333158
X-RAY DIFFRACTIONr_chiral_restr0.110.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8221.4351171
X-RAY DIFFRACTIONr_mcbond_other0.8161.4331170
X-RAY DIFFRACTIONr_mcangle_it1.4322.1471462
X-RAY DIFFRACTIONr_mcangle_other1.4322.151463
X-RAY DIFFRACTIONr_scbond_it0.7081.5672377
X-RAY DIFFRACTIONr_scbond_other0.7041.5672377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2032.3273527
X-RAY DIFFRACTIONr_long_range_B_refined2.98413.0494360
X-RAY DIFFRACTIONr_long_range_B_other2.98313.054360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 33 -
Rwork0.276 867 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79390.39220.17942.87121.7292.1508-0.0006-0.06990.0677-0.0423-0.00180.04-0.158-0.11970.00250.13760.0223-0.00940.13280.01720.01146.1207-0.8933-0.9327
21.6473-0.6644-0.83575.1322.53184.56350.0361-0.1660.48580.05880.00340.291-0.1865-0.3336-0.03950.178-0.0139-0.0170.2185-0.04880.1999-5.16-10.9485-16.0072
35.3974-0.64880.27242.61121.28967.0566-0.1161-0.6850.07440.3223-0.2685-0.1132-0.1197-0.73110.38450.3187-0.02870.0240.2042-0.04040.3209-2.335911.904818.0515
41.83680.06290.00223.63813.04194.40820.0196-0.1676-0.01590.0303-0.10710.3231-0.2601-0.60220.08750.27760.02730.01050.2221-0.02640.1577-3.013510.052212.909
56.60910.98882.31183.79183.73118.01980.00480.10460.0962-0.0542-0.24110.21150.1072-0.80680.23630.32690.0147-0.08470.1133-0.02290.1746-4.7878-14.4378-21.9424
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 300
2X-RAY DIFFRACTION2B1 - 14
3X-RAY DIFFRACTION3C15 - 25
4X-RAY DIFFRACTION4D1 - 15
5X-RAY DIFFRACTION5E16 - 25

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