- PDB-3vhw: Crystal structure of the human vitamin D receptor ligand binding ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 3vhw
Title
Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP
Components
Vitamin D3 receptor
Keywords
TRANSCRIPTION / HORMONE RECEPTOR
Function / homology
Function and homology information
regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding ...regulation of calcidiol 1-monooxygenase activity / positive regulation of vitamin D 24-hydroxylase activity / bile acid nuclear receptor activity / response to bile acid / Vitamin D (calciferol) metabolism / apoptotic process involved in mammary gland involution / phosphate ion transmembrane transport / positive regulation of apoptotic process involved in mammary gland involution / calcitriol binding / vitamin D response element binding / lithocholic acid binding / positive regulation of keratinocyte differentiation / positive regulation of vitamin D receptor signaling pathway / vitamin D receptor signaling pathway / intestinal absorption / bile acid signaling pathway / mammary gland branching involved in pregnancy / decidualization / negative regulation of keratinocyte proliferation / positive regulation of bone mineralization / nuclear retinoid X receptor binding / lactation / skeletal system development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / cell morphogenesis / intracellular calcium ion homeostasis / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / calcium ion transport / nuclear receptor activity / cell differentiation / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol Similarity search - Function
Resolution: 2.43→33.87 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 8.071 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.24696
557
4.8 %
RANDOM
Rwork
0.18908
-
-
-
obs
0.19191
11163
97.83 %
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all
-
11862
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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: 23.206 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.01 Å2
0 Å2
0 Å2
2-
-
0 Å2
0 Å2
3-
-
-
0.02 Å2
Refinement step
Cycle: LAST / Resolution: 2.43→33.87 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2022
0
41
95
2158
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.019
0.022
2106
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
2.119
2.009
2854
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
6.712
5
252
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
38.537
24.286
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
17.263
15
383
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
17.076
15
13
X-RAY DIFFRACTION
r_chiral_restr
0.196
0.2
328
X-RAY DIFFRACTION
r_gen_planes_refined
0.008
0.021
1552
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.893
1.5
1273
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.696
2
2070
X-RAY DIFFRACTION
r_scbond_it
2.713
3
833
X-RAY DIFFRACTION
r_scangle_it
4.43
4.5
784
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.434→2.497 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.28
36
-
Rwork
0.194
602
-
obs
-
-
74.45 %
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