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Open data
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Basic information
Entry | Database: PDB / ID: 5lux | ||||||
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Title | Homeobox transcription factor CDX1 bound to methylated DNA | ||||||
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![]() | TRANSCRIPTION / transcription factor / methylated DNA | ||||||
Function / homology | ![]() regulation of somitogenesis / methyl-CpG binding / bone morphogenesis / anterior/posterior axis specification / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding ...regulation of somitogenesis / methyl-CpG binding / bone morphogenesis / anterior/posterior axis specification / animal organ morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cell differentiation / 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 / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Morgunova, E. / Popov, A. / Taipale, J. | ||||||
![]() | ![]() Title: Impact of cytosine methylation on DNA binding specificities of human transcription factors. Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / ...Authors: Yin, Y. / Morgunova, E. / Jolma, A. / Kaasinen, E. / Sahu, B. / Khund-Sayeed, S. / Das, P.K. / Kivioja, T. / Dave, K. / Zhong, F. / Nitta, K.R. / Taipale, M. / Popov, A. / Ginno, P.A. / Domcke, S. / Yan, J. / Schubeler, D. / Vinson, C. / Taipale, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.9 KB | Display | ![]() |
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PDB format | ![]() | 114.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.4 KB | Display | ![]() |
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Full document | ![]() | 477.6 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 13.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ef6C ![]() 5egoC ![]() 5hodC ![]() 5ltyC ![]() 5ltxS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Components
-DNA chain , 4 types, 4 molecules ABFE
#1: DNA chain | Mass: 5173.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 5462.551 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#4: DNA chain | Mass: 5267.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#5: DNA chain | Mass: 5596.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Protein / Non-polymers , 2 types, 12 molecules KL![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#2: Protein | Mass: 7887.118 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG MME (5000),KCl, MgCl2, 2-Methyl propanol, Tris buffer |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9724 Å / Relative weight: 1 |
Reflection | Resolution: 3.23→58.12 Å / Num. obs: 5425 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 57 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.174 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 3.23→3.49 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.91 / CC1/2: 0.891 / % possible all: 88.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5LTX Resolution: 3.23→58.12 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.864 / SU B: 100.709 / SU ML: 0.697 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.729 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 237.96 Å2 / Biso mean: 90.603 Å2 / Biso min: 35.87 Å2
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Refinement step | Cycle: final / Resolution: 3.23→58.12 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 3.233→3.317 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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