[English] 日本語
![](img/lk-miru.gif)
- PDB-7sec: Crystal structure of human Fibrillarin in complex with compound 1a -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7sec | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human Fibrillarin in complex with compound 1a | |||||||||
![]() | rRNA 2'-O-methyltransferase fibrillarin | |||||||||
![]() | TRANSFERASE / Methyltransferase / S-adenosyl methionine | |||||||||
Function / homology | ![]() snoRNA localization / granular component / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / rRNA modification in the nucleus and cytosol / TFIID-class transcription factor complex binding / Major pathway of rRNA processing in the nucleolus and cytosol ...snoRNA localization / granular component / histone H2AQ104 methyltransferase activity / box C/D sno(s)RNA 3'-end processing / rRNA methyltransferase activity / box C/D methylation guide snoRNP complex / rRNA methylation / rRNA modification in the nucleus and cytosol / TFIID-class transcription factor complex binding / Major pathway of rRNA processing in the nucleolus and cytosol / Cajal body / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / fibrillar center / osteoblast differentiation / rRNA processing / ribosomal small subunit biogenesis / ATPase binding / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Shi, Y. / El-Deeb, I.M. / Masic, V. / Hartley-Tassell, L. / Maggioni, A. / von Itzstein, M. / Ve, T. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Discovery of Cofactor Competitive Inhibitors against the Human Methyltransferase Fibrillarin. Authors: Shi, Y. / El-Deeb, I.M. / Masic, V. / Hartley-Tassell, L. / Maggioni, A. / Itzstein, M.V. / Ve, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 186 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 146.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 19.6 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7se6C ![]() 7se7C ![]() 7se8C ![]() 7se9C ![]() 7seaC ![]() 7sebC ![]() 7sedC ![]() 2ipxS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 26681.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22087, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | ChemComp-FMT / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.14 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.75-3.3 M Sodium Formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→48.53 Å / Num. obs: 51310 / % possible obs: 99.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.81 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.034 / Rrim(I) all: 0.088 / Net I/σ(I): 7 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3233 / CC1/2: 0.894 / Rpim(I) all: 0.54 / Rrim(I) all: 1.21 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2IPX Resolution: 1.9→48.3 Å / SU ML: 0.2861 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.0438 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.98 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→48.3 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|