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Open data
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Basic information
Entry | Database: PDB / ID: 5o9j | ||||||||||||
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Title | Crystal structure of transcription factor IIB Mja mini-intein | ||||||||||||
![]() | Transcription initiation factor IIB,Transcription initiation factor IIB | ||||||||||||
![]() | HYDROLASE / Transcription factor IIB / mini-intein / HINT fold | ||||||||||||
Function / homology | ![]() transcription preinitiation complex assembly / intein-mediated protein splicing / intron homing / 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 | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Mikula, K.M. / Iwai, H. / Zhou, D. / Wlodawer, A. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95 KB | Display | ![]() |
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PDB format | ![]() | 71.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 486.8 KB | Display | ![]() |
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Full document | ![]() | 495.3 KB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o9iC ![]() 2cw8S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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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.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: tfb, MJ0782 / Production host: ![]() ![]() References: UniProt: Q58192, Hydrolases; Acting on ester bonds |
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-Non-polymers , 5 types, 225 molecules ![](data/chem/img/DIO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/MES.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DIO / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NH4 / #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.34 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→28.7 Å
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Refine LS restraints |
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LS refinement shell |
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