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Open data
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Basic information
Entry | Database: PDB / ID: 4g92 | ||||||
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Title | CCAAT-binding complex from Aspergillus nidulans with DNA | ||||||
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![]() | Transcription/DNA / transcription factor / nucleosome / minor groove binding / CCAAT-binding complex / histone fold motif / specific binding to the CCAAT-box / DNA / nucleus / Transcription-DNA complex | ||||||
Function / homology | ![]() CCAAT-binding factor complex / regulation of carbohydrate metabolic process / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription ...CCAAT-binding factor complex / regulation of carbohydrate metabolic process / nucleosome / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / DNA binding / nucleus Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, E.M. / Scharf, D.H. / Hortschansky, P. / Groll, M. / Brakhage, A.A. | ||||||
![]() | ![]() Title: DNA Minor Groove Sensing and Widening by the CCAAT-Binding Complex. Authors: Huber, E.M. / Scharf, D.H. / Hortschansky, P. / Groll, M. / Brakhage, A.A. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 158.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.6 KB | Display | ![]() |
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Full document | ![]() | 468.3 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g91SC 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
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 7669.910 Da / Num. of mol.: 1 / Fragment: UNP residues 231-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 10641.299 Da / Num. of mol.: 1 / Fragment: UNP residues 42-132 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 13666.752 Da / Num. of mol.: 1 / Fragment: UNP residues 47-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules DE
#4: DNA chain | Mass: 7574.896 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#5: DNA chain | Mass: 7780.062 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-Non-polymers , 2 types, 535 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, 0.2 M (NH4)2SO4, 25% PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2012 |
Radiation | Monochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 57233 / Num. obs: 54543 / % possible obs: 95.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.5 / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4G91 Resolution: 1.8→10 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.956 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.795 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.845 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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