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- PDB-4yhx: Crystal Structure of LAGLIDADG Meganuclease I-GpeMI Bound to Uncl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yhx | ||||||
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Title | Crystal Structure of LAGLIDADG Meganuclease I-GpeMI 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 | ![]() | 110.4 KB | Display | ![]() |
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PDB format | ![]() | 77.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.4 KB | Display | ![]() |
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Full document | ![]() | 446.8 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yisC ![]() 4yitC ![]() 4z1zC ![]() 4z20C ![]() 5espC ![]() 3qqyS 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
#1: Protein | Mass: 34857.055 Da / Num. of mol.: 1 / Fragment: unp residues 420-727 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: DNA chain | Mass: 8049.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#3: DNA chain | Mass: 8543.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 22.5% PEG 3000, 50mM CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ASYMMETRIC CURVED CRYSTAL Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.15→50 Å / Num. obs: 24373 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Rrim(I) all: 0.119 / Χ2: 1.181 / Net I/av σ(I): 11.281 / Net I/σ(I): 14.8 / Num. measured all: 84408 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3QQY Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.573 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.213 / 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: 173.39 Å2 / Biso mean: 36.192 Å2 / Biso min: 17.45 Å2
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Refinement step | Cycle: final / Resolution: 2.15→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.149→2.205 Å / Total num. of bins used: 20
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