+Open data
-Basic information
Entry | Database: PDB / ID: 3eik | ||||||
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Title | double stranded DNA binding protein | ||||||
Components | TATA-box-binding protein | ||||||
Keywords | TRANSCRIPTION / TATA box binding protein / DNA-binding / Initiation factor / Nucleus | ||||||
Function / homology | Function and homology information RNA polymerase II general transcription initiation factor activity / DNA-templated transcription initiation / DNA binding / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Encephalitozoon cuniculi (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Cui, S. / Wollmann, P. / Moldt, M. / Hopfner, K.-P. | ||||||
Citation | Journal: To be Published Title: structural studies of ecTBP Authors: Cui, S. / Wollmann, P. / Moldt, M. / Hopfner, K.-P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3eik.cif.gz | 166.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3eik.ent.gz | 131.6 KB | Display | PDB format |
PDBx/mmJSON format | 3eik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eik_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 3eik_full_validation.pdf.gz | 459.4 KB | Display | |
Data in XML | 3eik_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 3eik_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/3eik ftp://data.pdbj.org/pub/pdb/validation_reports/ei/3eik | HTTPS FTP |
-Related structure data
Related structure data | 1ytbS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24502.486 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Strain: GB-M1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8ST28 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES,2M NaCl,4% Acetone, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 18, 2008 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 41388 / Num. obs: 37329 / % possible obs: 90.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.03 % / Biso Wilson estimate: 25.23 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 2.99 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.44 / Num. unique all: 5640 / Rsym value: 0.326 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1YTB Resolution: 1.9→26.1 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.851 / SU ML: 0.31 / σ(F): 1.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.278 Å2 / ksol: 0.38 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 68.87 Å2 / Biso mean: 30.794 Å2 / Biso min: 13.2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→26.1 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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