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- PDB-1m5x: Crystal structure of the homing endonuclease I-MsoI bound to its ... -

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Basic information

Entry
Database: PDB / ID: 1m5x
TitleCrystal structure of the homing endonuclease I-MsoI bound to its DNA substrate
Components
  • 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
  • 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
  • DNA endonuclease I-MsoI
KeywordsHYDROLASE/DNA / LAGLIDADG / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


chloroplast / endonuclease activity
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) / Site-specific DNA endonuclease I-MsoI / :
Similarity search - Component
Biological speciesMonomastix sp. (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsChevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Flexible DNA Target Site Recognition by Divergent Homing Endonuclease Isoschizomers I-CreI and I-MsoI
Authors: Chevalier, B. / Turmel, M. / Lemieux, C. / Monnat, R.J. / Stoddard, B.L.
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Feb 14, 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 / struct_site
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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'
D: 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'
A: DNA endonuclease I-MsoI
B: DNA endonuclease I-MsoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8057
Polymers53,6844
Non-polymers1203
Water4,125229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.510, 42.210, 71.320
Angle α, β, γ (deg.)73.34, 73.17, 71.09
Int Tables number1
Space group name H-MP1

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Components

#1: DNA chain 5'-D(*GP*CP*AP*GP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3'


Mass: 7419.792 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: target DNA (Watson strand)
#2: DNA chain 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*CP*TP*GP*C)-3'


Mass: 7321.716 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: target DNA (Crick strand)
#3: Protein DNA endonuclease I-MsoI


Mass: 19471.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monomastix sp. (plant) / Strain: OKE-1 / Plasmid: pI-MsoI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q8WKW7, UniProt: C0JWR6*PLUS
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, sodium chloride, calcium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 40011
2NaClSodium chloride11
3CaCl211
4NaClSodium chloride12
5CaCl212
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.9 / PH range high: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
119-22 %PEG4001reservoir
2100 mMTris1reservoirpH7.3-7.9
310 mM1reservoirCaCl2
420 mM1reservoirNaCl
53.5 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorDetector: CCD / Date: Mar 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 20335 / % possible obs: 97.6 % / Biso Wilson estimate: 23.2 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 26.1
Reflection shellResolution: 2.25→2.39 Å / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 9.79 / % possible all: 96.9
Reflection
*PLUS
Num. obs: 19849 / % possible obs: 97.5 % / Num. measured all: 38547 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: poly ananine I-CreI/DNA complex

Resolution: 2.25→19.96 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 881264.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 956 4.8 %RANDOM
Rwork0.219 ---
obs-19849 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.7588 Å2 / ksol: 0.352117 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.08 Å2-6.22 Å24.61 Å2
2--4.05 Å29.45 Å2
3----11.12 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2612 978 3 229 3822
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d1.17
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.352
X-RAY DIFFRACTIONc_scbond_it1.92
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 184 5.6 %
Rwork0.266 3112 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.253 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.22
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.17

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