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: 1.3→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.377 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19897
3652
5 %
RANDOM
Rwork
0.1792
-
-
-
all
0.18018
68780
-
-
obs
0.18018
68780
95.12 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parameters
Biso mean: 17.054 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.52 Å2
0 Å2
0 Å2
2-
-
0.16 Å2
0 Å2
3-
-
-
0.36 Å2
Refinement step
Cycle: LAST / Resolution: 1.3→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2017
0
35
275
2327
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.008
0.022
2127
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1476
X-RAY DIFFRACTION
r_angle_refined_deg
1.297
2.004
2888
X-RAY DIFFRACTION
r_angle_other_deg
0.859
3
3623
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
4.864
5
262
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.53
24.066
91
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
11.451
15
391
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.251
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.067
0.2
332
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
2299
X-RAY DIFFRACTION
r_gen_planes_other
0.005
0.02
402
LS refinement shell
Resolution: 1.301→1.334 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.249
205
-
Rwork
0.241
4299
-
obs
-
-
84.05 %
Refinement TLS params.
Method: refined / Origin x: -13.3956 Å / Origin y: -5.4449 Å / Origin z: 24.2584 Å
11
12
13
21
22
23
31
32
33
T
0.0159 Å2
0 Å2
-0.0083 Å2
-
0.0053 Å2
0.0043 Å2
-
-
0.0185 Å2
L
0.5191 °2
0.171 °2
0.3059 °2
-
0.3719 °2
0.0898 °2
-
-
0.6878 °2
S
-0.0172 Å °
0.0376 Å °
0.0485 Å °
-0.036 Å °
-0.0083 Å °
0.0056 Å °
-0.0133 Å °
-0.0005 Å °
0.0255 Å °
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi