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Yorodumi- PDB-2c6y: Crystal structure of interleukin enhancer-binding factor 1 bound ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c6y | ||||||
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Title | Crystal structure of interleukin enhancer-binding factor 1 bound to DNA | ||||||
Components |
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Keywords | TRANSCRIPTION REGULATION / DNA-BINDING DOMAIN / FORKHEAD TRANSCRIPTION FACTORS / INTERLEUKIN ENHANCER BINDING FACTOR / WINGED HELIX / FORKHEAD | ||||||
Function / homology | Function and homology information canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding ...canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Tsai, K.-L. / Huang, C.-Y. / Chang, C.-H. / Sun, Y.-J. / Chuang, W.-J. / Hsiao, C.-D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins. Authors: Tsai, K.-L. / Huang, C.-Y. / Chang, C.-H. / Sun, Y.-J. / Chuang, W.-J. / Hsiao, C.-D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c6y.cif.gz | 72.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c6y.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 2c6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/2c6y ftp://data.pdbj.org/pub/pdb/validation_reports/c6/2c6y | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 12812.529 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 251-348 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q01167 #2: DNA chain | | Mass: 4905.229 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 5'-D(*TP*GP*TP*TP*GP*TP*AP*AP*AP*CP*AP*AP* TP*AP*CP*A)-3' Source: (synth.) HOMO SAPIENS (human) #3: DNA chain | | Mass: 4887.201 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 5'-D(*AP*TP*GP*TP*AP*TP*TP*GP*TP*TP*TP*AP* CP*AP*AP*C)-3' Source: (synth.) HOMO SAPIENS (human) #4: Chemical | #5: Water | ChemComp-HOH / | Sequence details | RESIDUE NUMBER BEFORE 1 IS T7 TAG. THE T7 TAGS IN BOTH CHAIN A AND B ARE DISORDERED, AND NOT ...RESIDUE NUMBER BEFORE 1 IS T7 TAG. THE T7 TAGS IN BOTH CHAIN A AND B ARE DISORDERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.4 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.12714 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12714 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→29.44 Å / Num. obs: 12691 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 45.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→29.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 577606.57 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: RESIDUE 96-98 IN CHAIN B ARE DISORDERED, AND NOT DETERMINED IN THE MODEL.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.5238 Å2 / ksol: 0.430544 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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