+Open data
-Basic information
Entry | Database: PDB / ID: 5o9j | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of transcription factor IIB Mja mini-intein | ||||||||||||
Components | Transcription initiation factor IIB,Transcription initiation factor IIB | ||||||||||||
Keywords | HYDROLASE / Transcription factor IIB / mini-intein / HINT fold | ||||||||||||
Function / homology | Function and homology information transcription preinitiation complex assembly / intron homing / intein-mediated protein splicing / transcription preinitiation complex / TBP-class protein binding / DNA-templated transcription initiation / endonuclease activity / Hydrolases; Acting on ester bonds / DNA-binding transcription factor activity / zinc ion binding Similarity search - Function | ||||||||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Mikula, K.M. / Iwai, H. / Zhou, D. / Wlodawer, A. | ||||||||||||
Funding support | Finland, United States, 3items
| ||||||||||||
Citation | Journal: J. Mol. Biol. / Year: 2017 Title: Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins. Authors: Iwai, H. / Mikula, K.M. / Oeemig, J.S. / Zhou, D. / Li, M. / Wlodawer, A. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5o9j.cif.gz | 95 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5o9j.ent.gz | 71.1 KB | Display | PDB format |
PDBx/mmJSON format | 5o9j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/5o9j ftp://data.pdbj.org/pub/pdb/validation_reports/o9/5o9j | HTTPS FTP |
---|
-Related structure data
Related structure data | 5o9iC 2cw8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20872.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tfb, MJ0782 / Production host: Escherichia coli (E. coli) References: UniProt: Q58192, Hydrolases; Acting on ester bonds |
---|
-Non-polymers , 5 types, 225 molecules
#2: Chemical | ChemComp-DIO / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NH4 / #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, dioxane, ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→28.7 Å / Num. obs: 30100 / % possible obs: 95.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.6 |
Reflection shell | Highest resolution: 2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.6 / % possible all: 92.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CW8 Resolution: 2→28.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.92
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|