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- PDB-7sea: Crystal structure of human Fibrillarin in complex with compound 2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7sea | |||||||||
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Title | Crystal structure of human Fibrillarin in complex with compound 2 from cocktail soak | |||||||||
![]() | 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 121.9 KB | Display | ![]() |
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PDB format | ![]() | 76.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 771.3 KB | Display | ![]() |
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Full document | ![]() | 771.8 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7se6C ![]() 7se7C ![]() 7se8C ![]() 7se9C ![]() 7sebC ![]() 7secC ![]() 7sedC ![]() 2ipxS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26681.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P22087, Transferases; Transferring one-carbon groups; Methyltransferases | ||||||||
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#2: Chemical | ChemComp-FMT / #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-8XF / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.76 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 7, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→47.96 Å / Num. obs: 25161 / % possible obs: 99.8 % / Redundancy: 7.3 % / Biso Wilson estimate: 27.34 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.063 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.91→1.95 Å / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1639 / CC1/2: 0.865 / Rpim(I) all: 0.334 / Rrim(I) all: 0.899 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2IPX Resolution: 1.91→45.27 Å / SU ML: 0.2289 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.9043 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.91→45.27 Å
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Refine LS restraints |
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LS refinement shell |
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