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Yorodumi- PDB-5e5o: I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions -
+Open data
-Basic information
Entry | Database: PDB / ID: 5e5o | ||||||
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Title | I-SmaMI bound to uncleaved DNA target in the presence of Calcium ions | ||||||
Components |
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Keywords | HYDROLASE/DNA / LAGLIDADG / I-SmaMI / Complex / uncleaved / HYDROLASE-DNA complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sordaria macrospora (fungus) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å | ||||||
Authors | Shen, B.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e5o.cif.gz | 194.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e5o.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 5e5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e5o_validation.pdf.gz | 453.7 KB | Display | wwPDB validaton report |
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Full document | 5e5o_full_validation.pdf.gz | 459.8 KB | Display | |
Data in XML | 5e5o_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 5e5o_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/5e5o ftp://data.pdbj.org/pub/pdb/validation_reports/e5/5e5o | HTTPS FTP |
-Related structure data
Related structure data | 5e5pC 5e5sC 5e63C 5e67C 4loxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34155.707 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 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 7691.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: DNA chain | Mass: 7664.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 90 molecules
#4: Chemical | #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.23 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG MME550, HEPES / PH range: 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Sep 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→27 Å / Num. obs: 17265 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 6.9 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LOX Resolution: 2.36→27 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.911 / SU B: 23.483 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.537 / ESU R Free: 0.303 / 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: 41.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2.36→27 Å
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Refine LS restraints |
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