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- PDB-4yis: Crystal Structure of LAGLIDADG Meganuclease I-CpaMI Bound to Uncl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yis | ||||||
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Title | Crystal Structure of LAGLIDADG Meganuclease I-CpaMI Bound to Uncleaved DNA | ||||||
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![]() | hydrolase/dna / Hydrolase-DNA complex / LAGLIDADG / homing endonuclease / meganuclease | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Hallinan, J.P. / Kaiser, B.K. / Stoddard, B.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity. Authors: Lambert, A.R. / Hallinan, J.P. / Shen, B.W. / Chik, J.K. / Bolduc, J.M. / Kulshina, N. / Robins, L.I. / Kaiser, B.K. / Jarjour, J. / Havens, K. / Scharenberg, A.M. / Stoddard, B.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 191.7 KB | Display | ![]() |
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PDB format | ![]() | 143.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.7 KB | Display | ![]() |
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Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 33.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yhxC ![]() 4yitC ![]() 4z1zC ![]() 4z20C ![]() 5espC ![]() 3qqyS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33652.527 Da / Num. of mol.: 2 / Fragment: unp residues 122-416 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: mtSrRNA I4 / Production host: ![]() ![]() |
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-DNA chain , 2 types, 4 molecules ECFD
#2: DNA chain | Mass: 8439.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 8747.621 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 3 types, 47 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.56 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 26% PEG 3350, 5mM DDT, 5mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: May 6, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Varimax HF Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 23588 / % possible obs: 94.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.101 / Χ2: 1.368 / Net I/av σ(I): 8.473 / Net I/σ(I): 13.3 / Num. measured all: 74772 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 3QQY Resolution: 2.89→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 21.579 / SU ML: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.48 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 105.46 Å2 / Biso mean: 41.837 Å2 / Biso min: 22.94 Å2
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Refinement step | Cycle: final / Resolution: 2.89→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.89→2.965 Å / Total num. of bins used: 20
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