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- PDB-3a2h: Crystal structure of the rat vitamin D receptor ligand binding do... -
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Basic information
Entry | Database: PDB / ID: 3a2h | ||||||
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Title | Crystal structure of the rat vitamin D receptor ligand binding domain complexed with TEI-9647 and a synthetic peptide containing the NR2 box of DRIP 205 | ||||||
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Function / homology | ![]() enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition ...enucleate erythrocyte development / positive regulation of type II interferon-mediated signaling pathway / negative regulation of bone trabecula formation / Vitamin D (calciferol) metabolism / regulation of RNA biosynthetic process / androgen biosynthetic process / positive regulation of G0 to G1 transition / retinal pigment epithelium development / mammary gland branching involved in thelarche / G0 to G1 transition / SUMOylation of intracellular receptors / thyroid hormone mediated signaling pathway / Nuclear Receptor transcription pathway / bile acid nuclear receptor activity / response to bile acid / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kakuda, S. / Takimoto-Kamimura, M. | ||||||
![]() | ![]() Title: Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1alpha-hydroxyvitamin D(3)-26,23-lactone Authors: Kakuda, S. / Ishizuka, S. / Eguchi, H. / Mizwicki, M.T. / Norman, A.W. / Takimoto-Kamimura, M. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.1 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3a2iC ![]() 3a2jC ![]() 1rk3S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30055.498 Da / Num. of mol.: 1 / Fragment: ligand binding domain, residues 116-423 / Mutation: DEL(165-211) mutant Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1570.898 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-TEJ / ( |
#4: Water | ChemComp-HOH / ![]() |
Nonpolymer details | THE LIGAND TEJ CAN BE CALLED AS TEI-9647. |
Sequence details | THIS PROTEIN VITAMIN D3 RECEPTOR IS A DELETION MUTANT. THE RESIDUES 165-211 WERE DELETED. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.15 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.2M malonic acid, pH 7.0, VAPOR DIFFUSION, HANGING 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: Sep 18, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.5→50 Å / Num. obs: 9008 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 8.2 / Num. measured all: 28263 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3.3 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1rk3 Resolution: 2.5→40.36 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.854 / SU B: 11.654 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 1.311 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.112 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→40.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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