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Yorodumi- PDB-7seb: Crystal structure of human Fibrillarin in complex with compound 2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7seb | |||||||||
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Title | Crystal structure of human Fibrillarin in complex with compound 2 from single soak | |||||||||
Components | rRNA 2'-O-methyltransferase fibrillarin | |||||||||
Keywords | TRANSFERASE / Methyltransferase / S-adenosyl methionine | |||||||||
Function / homology | Function and homology information U6 snRNA 2'-O-ribose methyltransferase activity / 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 / Cajal body ...U6 snRNA 2'-O-ribose methyltransferase activity / 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 / Cajal body / TFIID-class transcription factor complex binding / Major pathway of rRNA processing in the nucleolus and cytosol / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / fibrillar center / osteoblast differentiation / rRNA processing / ATPase binding / ribosomal small subunit biogenesis / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | |||||||||
Authors | Shi, Y. / El-Deeb, I.M. / Masic, V. / Hartley-Tassell, L. / Maggioni, A. / von Itzstein, M. / Ve, T. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Pharmaceuticals / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7seb.cif.gz | 123 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7seb.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 7seb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7seb_validation.pdf.gz | 759.6 KB | Display | wwPDB validaton report |
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Full document | 7seb_full_validation.pdf.gz | 759.8 KB | Display | |
Data in XML | 7seb_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 7seb_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/7seb ftp://data.pdbj.org/pub/pdb/validation_reports/se/7seb | HTTPS FTP |
-Related structure data
Related structure data | 7se6C 7se7C 7se8C 7se9C 7seaC 7secC 7sedC 2ipxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: FBL, FIB1, FLRN / Production host: Escherichia coli (E. coli) References: UniProt: P22087, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-8XF / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
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: 1.8→48.03 Å / Num. obs: 29246 / % possible obs: 97.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 29.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.023 / Rrim(I) all: 0.081 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1359 / CC1/2: 0.745 / Rpim(I) all: 0.495 / Rrim(I) all: 1.733 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IPX Resolution: 1.81→48.03 Å / SU ML: 0.2244 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.9387 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: 36.71 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→48.03 Å
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Refine LS restraints |
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LS refinement shell |
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