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Open data
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Basic information
Entry | Database: PDB / ID: 5.0E+63 | ||||||
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Title | K262A mutant of I-SmaMI | ||||||
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![]() | Hydrolase/DNA / LAGLIDADG / I-SmaMI / K262A / mutant / Hydrolase-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Shen, B. / Stoddard, B. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.9 KB | Display | ![]() |
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PDB format | ![]() | 144.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.9 KB | Display | ![]() |
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Full document | ![]() | 482.1 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5e5oC ![]() 5e5pC ![]() 5e5sC ![]() 5e67C ![]() 4loxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | 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.) ![]() Strain: ATCC MYA-333 / DSM 997 / K(L3346) / K-hell / Gene: SMAC_12671 / Plasmid: pET21d(+) / Production host: ![]() ![]() |
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-DNA chain , 4 types, 4 molecules BCDE
#2: DNA chain | Mass: 4248.794 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 3398.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: DNA chain | Mass: 4534.958 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#5: DNA chain | Mass: 3085.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 4 types, 54 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/MXE.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MXE.gif)
![](data/chem/img/PG0.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Chemical | ChemComp-MXE / | #8: Chemical | ChemComp-PG0 / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 38.68 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 28-32% PEGMME550, HEPES Mg++ / PH range: 7.5-8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Apr 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: 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
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.838 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→30 Å
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Refine LS restraints |
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