- PDB-4e2j: X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor ... -
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Basic information
Entry
Database: PDB / ID: 4e2j
Title
X-Ray Crystal Structure of the Ancestral Glucocorticoid Receptor 2 ligand binding domain in complex with mometasone furoate and TIF-2 coactivator fragment
RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol ...RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / Regulation of lipid metabolism by PPARalpha / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / response to progesterone / nuclear receptor binding / circadian regulation of gene expression / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / Circadian Clock / HATs acetylate histones / Estrogen-dependent gene expression / transcription regulator complex / transcription coactivator activity / nuclear body / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm Similarity search - Function
Resolution: 2.5→45.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.153 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): 5.3 / ESU R: 0.325 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.25483
1545
5 %
RANDOM
Rwork
0.20451
-
-
-
all
0.20706
30710
-
-
obs
0.20706
29118
99.9 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 45.186 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
-0 Å2
2-
-
0 Å2
-0 Å2
3-
-
-
-0 Å2
Refinement step
Cycle: LAST / Resolution: 2.5→45.19 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4179
0
85
151
4415
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.005
0.02
4372
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.078
2.004
5915
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.084
5
515
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.068
24.316
190
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.402
15
810
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
16.059
15
23
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
663
X-RAY DIFFRACTION
r_gen_planes_refined
0.003
0.021
3183
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
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
X-RAY DIFFRACTION
r_scbond_it
X-RAY DIFFRACTION
r_scangle_it
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.501→2.566 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.399
93
-
Rwork
0.279
2099
-
obs
-
-
98.96 %
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