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Open data
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Basic information
Entry | Database: PDB / ID: 6xzi | ||||||||||||
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Title | Structure of zVDR LBD-calcitriol in complex with chimera 11 | ||||||||||||
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![]() | GENE REGULATION / Nuclear Receptor / Foldamer / helix mimicry / Protein-Protein Interaction | ||||||||||||
Function / homology | ![]() heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis ...heart jogging / Vitamin D (calciferol) metabolism / SUMOylation of intracellular receptors / vitamin D binding / calcitriol binding / vitamin D response element binding / lithocholic acid binding / hematopoietic stem cell proliferation / heart looping / calcium ion homeostasis / ossification / nuclear receptor activity / cell differentiation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Buratto, J. / Belorusova, A.Y. / Rochel, N. / Guichard, G. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Basis for alpha-Helix Mimicry and Inhibition of Protein-Protein Interactions with Oligourea Foldamers. Authors: Cussol, L. / Mauran-Ambrosino, L. / Buratto, J. / Belorusova, A.Y. / Neuville, M. / Osz, J. / Fribourg, S. / Fremaux, J. / Dolain, C. / Goudreau, S.R. / Rochel, N. / Guichard, G. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121 KB | Display | ![]() |
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PDB format | ![]() | 90.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 761.7 KB | Display | ![]() |
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Full document | ![]() | 765 KB | Display | |
Data in XML | ![]() | 12.6 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6hfaC ![]() 6xzhC ![]() 6xzjC ![]() 6xzkC ![]() 6xzvC ![]() 2hc4S 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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Unit cell |
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Components
#1: Protein | Mass: 34060.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1111.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-VDX / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.1 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / Details: NH4Acetate 3.5M, 0.1 M Tris pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→22.802 Å / Num. obs: 20986 / % possible obs: 99.52 % / Redundancy: 7.3 % / Rpim(I) all: 0.032 / Net I/σ(I): 14.93 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2018 / Rpim(I) all: 0.472 / % possible all: 99.11 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2HC4 Resolution: 2.1→22.802 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 156.56 Å2 / Biso mean: 57.6826 Å2 / Biso min: 31.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→22.802 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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