negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / monoatomic ion homeostasis ...negative regulation of cell-cell adhesion mediated by integrin / lymphocyte migration into lymph node / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of termination of RNA polymerase II transcription / monoatomic cation homeostasis / negative regulation of pancreatic juice secretion / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / positive regulation of mitotic cytokinesis / negative regulation of sodium ion transport / monoatomic ion homeostasis / regulation of mRNA export from nucleus / positive regulation of potassium ion import across plasma membrane / regulation of sodium ion transmembrane transport / intracellular chloride ion homeostasis / negative regulation of heterotypic cell-cell adhesion / positive regulation of T cell chemotaxis / positive regulation of systemic arterial blood pressure / non-membrane-bounded organelle assembly / potassium ion homeostasis / cellular response to chemokine / potassium channel inhibitor activity / protein serine/threonine kinase inhibitor activity / negative regulation of leukocyte cell-cell adhesion / cellular hyperosmotic response / regulation of monoatomic cation transmembrane transport / cell volume homeostasis / negative regulation of protein localization to plasma membrane / intracellular non-membrane-bounded organelle / protein kinase activator activity / sodium ion transmembrane transport / GABA-ergic synapse / phosphatase binding / monoatomic ion transport / regulation of sodium ion transport / negative regulation of protein ubiquitination / cellular response to calcium ion / negative regulation of autophagy / molecular condensate scaffold activity / modulation of chemical synaptic transmission / mitotic spindle / regulation of blood pressure / positive regulation of angiogenesis / positive regulation of canonical Wnt signaling pathway / heart development / T cell receptor signaling pathway / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / protein kinase binding / magnesium ion binding / signal transduction / protein-containing complex / ATP binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function
Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase OSR1/WNK, CCT domain / Oxidative-stress-responsive kinase 1 C-terminal domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta Similarity search - Domain/homology
Resolution: 3.5→43.409 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.88 / SU B: 87.762 / SU ML: 0.633 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.882 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.29743
364
10 %
RANDOM
Rwork
0.2428
-
-
-
obs
0.24827
3290
99.37 %
-
all
-
3680
-
-
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: 114.639 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.31 Å2
-0 Å2
-0.05 Å2
2-
-
0.58 Å2
0 Å2
3-
-
-
-0.26 Å2
Refinement step
Cycle: LAST / Resolution: 3.5→43.409 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2180
0
1
9
2190
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.004
0.019
2222
X-RAY DIFFRACTION
r_angle_refined_deg
0.753
1.969
2985
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
3.369
5
270
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
30.096
23.505
97
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.214
15
431
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
12.228
15
16
X-RAY DIFFRACTION
r_chiral_restr
0.049
0.2
329
X-RAY DIFFRACTION
r_gen_planes_refined
0.002
0.021
1628
X-RAY DIFFRACTION
r_mcbond_it
0.718
7.311
1083
X-RAY DIFFRACTION
r_mcangle_it
1.33
10.967
1352
X-RAY DIFFRACTION
r_scbond_it
0.537
7.355
1139
X-RAY DIFFRACTION
r_long_range_B_refined
4.581
60.341
3326
LS refinement shell
Resolution: 3.5→3.591 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.27
25
-
Rwork
0.265
233
-
obs
-
-
100 %
Refinement TLS params.
Method: refined / Origin x: 13.3208 Å / Origin y: 0.3161 Å / Origin z: 17.265 Å
11
12
13
21
22
23
31
32
33
T
0.1317 Å2
-0.0102 Å2
0.0043 Å2
-
0.1224 Å2
-0.0304 Å2
-
-
0.0737 Å2
L
4.9451 °2
-0.0024 °2
0.7294 °2
-
7.0864 °2
1.9396 °2
-
-
5.879 °2
S
0.0176 Å °
0.5792 Å °
-0.28 Å °
-0.96 Å °
0.0721 Å °
-0.0478 Å °
-0.3181 Å °
-0.1995 Å °
-0.0897 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