+Open data
-Basic information
Entry | Database: PDB / ID: 5fai | ||||||
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Title | EMG1 N1-Specific Pseudouridine Methyltransferase | ||||||
Components | Ribosomal RNA small subunit methyltransferase NEP1 | ||||||
Keywords | TRANSFERASE / EMG1 / Methyltransferase / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information nucleologenesis / rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / rRNA modification in the nucleus and cytosol / blastocyst development / Major pathway of rRNA processing in the nucleolus and cytosol / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing ...nucleologenesis / rRNA (pseudouridine) methyltransferase activity / rRNA base methylation / rRNA modification in the nucleus and cytosol / blastocyst development / Major pathway of rRNA processing in the nucleolus and cytosol / Transferases; Transferring one-carbon groups; Methyltransferases / small-subunit processome / ribosomal small subunit biogenesis / rRNA processing / chromosome / rRNA binding / nucleolus / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | DONG, A. / ZENG, H. / LI, Y. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: EMG1 N1-Specific Pseudouridine Methyltransferase Authors: ZENG, H. / DONG, A. / LI, Y. / TEMPEL, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fai.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fai.ent.gz | 45.5 KB | Display | PDB format |
PDBx/mmJSON format | 5fai.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/5fai ftp://data.pdbj.org/pub/pdb/validation_reports/fa/5fai | HTTPS FTP |
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-Related structure data
Related structure data | 2v3kS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 25367.537 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EMG1, C2F / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus RIL References: UniProt: Q92979, Transferases; Transferring one-carbon groups; Methyltransferases | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | #4: Chemical | ChemComp-UNX / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M di-NH4 Citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 26058 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1.294 / Net I/av σ(I): 26.862 / Net I/σ(I): 8.4 / Num. measured all: 181554 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V3K Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.208 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 66.44 Å2 / Biso mean: 23.676 Å2 / Biso min: 13.92 Å2
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Refinement step | Cycle: final / Resolution: 1.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.802→1.848 Å / Total num. of bins used: 20
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