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- PDB-5e5p: Wild type I-SmaMI in the space group of C121 -

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Basic information

Entry
Database: PDB / ID: 5e5p
TitleWild type I-SmaMI in the space group of C121
ComponentsI-SmaMI LAGLIDADG meganuclease
KeywordsHYDROLASE / LAGLIDADG / I-SmaMI
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
Homing endonuclease LAGLIDADG domain-containing protein
Similarity search - Component
Biological speciesSordaria macrospora (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsShen, B.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM105691 United States
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 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: pdbx_entity_src_syn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: I-SmaMI LAGLIDADG meganuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3974
Polymers34,1531
Non-polymers2443
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint11 kcal/mol
Surface area16870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.327, 58.230, 42.046
Angle α, β, γ (deg.)90.00, 96.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein I-SmaMI LAGLIDADG meganuclease


Mass: 34152.641 Da / Num. of mol.: 1 / Fragment: UNP residues 114-415
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)RIL+ / References: UniProt: F7WD42
#2: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% PEG8K, HEPES / PH range: 7.5

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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: Sep 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.64→27.1 Å / Num. obs: 10491 / % possible obs: 98.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 21.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 22
Reflection shellResolution: 2.64→2.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 7.5 / % possible all: 87

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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: 2.65→27.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.866 / SU B: 23.617 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R: 3.427 / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 495 4.8 %RANDOM
Rwork0.17521 ---
obs0.17919 9875 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å21.46 Å2
2--0.99 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 2.65→27.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 16 84 2457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192424
X-RAY DIFFRACTIONr_bond_other_d0.0020.022394
X-RAY DIFFRACTIONr_angle_refined_deg2.1051.9713255
X-RAY DIFFRACTIONr_angle_other_deg1.09835531
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2065294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84424.44499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04115455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.934158
X-RAY DIFFRACTIONr_chiral_restr0.1170.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022659
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02549
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_it1.2831.951179
X-RAY DIFFRACTIONr_mcbond_other1.2821.9461178
X-RAY DIFFRACTIONr_mcangle_it2.2842.9151472
X-RAY DIFFRACTIONr_mcangle_other2.2832.9191473
X-RAY DIFFRACTIONr_scbond_it0.9972.0661245
X-RAY DIFFRACTIONr_scbond_other0.9972.0661245
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7823.0211784
X-RAY DIFFRACTIONr_long_range_B_refined3.60414.8712712
X-RAY DIFFRACTIONr_long_range_B_other3.60314.8842713
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 27 -
Rwork0.241 616 -
obs--87.84 %
Refinement TLS params.Method: refined / Origin x: -22.7108 Å / Origin y: -24.5672 Å / Origin z: 15.7675 Å
111213212223313233
T0.0129 Å2-0.0085 Å2-0.0151 Å2-0.013 Å20.019 Å2--0.0661 Å2
L2.0782 °2-0.9463 °2-1.3542 °2-1.5358 °20.9836 °2--1.8575 °2
S-0.0253 Å °0.0657 Å °-0.1519 Å °-0.0889 Å °-0.0113 Å °0.1071 Å °-0.0041 Å °-0.0472 Å °0.0366 Å °

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