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Open data
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Basic information
Entry | Database: PDB / ID: 1mk0 | ||||||
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Title | catalytic domain of intron endonuclease I-TevI, E75A mutant | ||||||
![]() | Intron-associated endonuclease 1 | ||||||
![]() | HYDROLASE / alpha/beta fold / CATALYTIC DOMAIN / DNA-BINDING SURFACE | ||||||
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 | ![]() | 33.2 KB | Display | ![]() |
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PDB format | ![]() | 24.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.3 KB | Display | ![]() |
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Full document | ![]() | 444.5 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 12 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ln0SC 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: 11406.057 Da / Num. of mol.: 1 / Fragment: catalytic domain (residues 1 to 97) / Mutation: E75A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P13299, Hydrolases; Acting on ester bonds |
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#2: Chemical | ChemComp-CIT / |
#3: Chemical | ChemComp-BME / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6 M sodium citrate, 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: Jul 11, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 15342 / Num. obs: 15342 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 84 |
Reflection shell | Resolution: 1.6→1.65 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 12 / % possible all: 98.3 |
Reflection | *PLUS Lowest resolution: 50 Å / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 98.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 23.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1LN0 Resolution: 1.6→36.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1085373.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.2046 Å2 / ksol: 0.393289 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.6 Å2
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Refine analyze | Luzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.11 Å | ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→36.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.216 / Rfactor Rwork: 0.197 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.262 / Rfactor Rwork: 0.229 |