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Open data
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Basic information
Entry | Database: PDB / ID: 1ln0 | ||||||
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Title | Structure of the Catalytic Domain of Homing Endonuclease I-TevI | ||||||
![]() | intron-associated endonuclease 1 | ||||||
![]() | HYDROLASE / alpha/beta fold | ||||||
Function / homology | ![]() double-stranded DNA endonuclease activity / nucleic acid metabolic process / intron homing / DNA-binding transcription repressor activity / transcription repressor complex / endonuclease activity / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / negative regulation of DNA-templated transcription / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Van Roey, P. / Meehan, L. / Kowalski, J.C. / Belfort, M. / Derbyshire, V. | ||||||
![]() | ![]() Title: Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Authors: Van Roey, P. / Meehan, L. / Kowalski, J.C. / Belfort, M. / Derbyshire, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.9 KB | Display | ![]() |
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PDB format | ![]() | 40.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.1 KB | Display | ![]() |
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Full document | ![]() | 440.2 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | dimer of domain covalently linked by disulfide bridge between Cys39 residues |
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Components
#1: Protein | Mass: 11377.977 Da / Num. of mol.: 2 / Fragment: catalytic domain (residues 1 to 97) / Mutation: R27A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13299, Hydrolases; Acting on ester bonds #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 22% PEG8000, 0.1 M MES, 5% ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: BRANDEIS - B1.2 / Detector: CCD / Date: Aug 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 16242 / Num. obs: 15982 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.73 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.4 |
Reflection shell | Resolution: 2→2.1 Å / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 8.3 / % possible all: 61.6 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 16242 |
Reflection shell | *PLUS % possible obs: 61.6 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.2 |