+Open data
-Basic information
Entry | Database: PDB / ID: 4rg1 | ||||||
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Title | Methyltransferase domain of C9orf114 | ||||||
Components | C9orf114 | ||||||
Keywords | TRANSFERASE / C9orf114 / Methyltransferase / SAH / structural genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information kinetochore => GO:0000776 / maintenance of centrosome location / miRNA processing / spindle pole centrosome / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / mitotic spindle / kinetochore ...kinetochore => GO:0000776 / maintenance of centrosome location / miRNA processing / spindle pole centrosome / miRNA binding / post-transcriptional regulation of gene expression / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / mitotic spindle / kinetochore / methylation / cell cycle / cell division / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | ||||||
Authors | Dong, A. / Zeng, H. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Human C9orf114 in complex with S-adenosyl-homocysteine Authors: Zeng, H. / Dong, A. / Walker, J.R. / Li, Y. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Brown, P.J. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rg1.cif.gz | 150.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rg1.ent.gz | 111 KB | Display | PDB format |
PDBx/mmJSON format | 4rg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rg/4rg1 ftp://data.pdbj.org/pub/pdb/validation_reports/rg/4rg1 | HTTPS FTP |
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-Related structure data
Related structure data | 1k3rS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34282.582 Da / Num. of mol.: 2 / Fragment: methyltransferase domain (UNP residues 64-376) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf114 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Codon Plus RIL / References: UniProt: Q5T280 |
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-Non-polymers , 5 types, 597 molecules
#2: Chemical | #3: Chemical | ChemComp-15P / #4: Chemical | #5: Chemical | ChemComp-PGO / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 28% PEG3350, 0.2 M diammonium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2014 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock high-resolution double-crystal Si(111) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.86→50 Å / Num. all: 64378 / Num. obs: 64378 / % possible obs: 100 % / Redundancy: 8.4 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.099 / Χ2: 1.077 / Net I/σ(I): 24 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: PDB ENTRY 1K3R Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.197 / WRfactor Rwork: 0.1577 / FOM work R set: 0.8236 / SU B: 2.747 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1153 / SU Rfree: 0.1137 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 86.46 Å2 / Biso mean: 24.781 Å2 / Biso min: 12.07 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.908 Å / Total num. of bins used: 20
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