+Open data
-Basic information
Entry | Database: PDB / ID: 2b9e | ||||||
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Title | Human NSUN5 protein | ||||||
Components | NOL1/NOP2/Sun domain family, member 5 isoform 2 | ||||||
Keywords | TRANSFERASE / methytransferase / NOL1/NOP2/Sun domain family / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information rRNA (cytosine-C5-)-methyltransferase activity / oligodendrocyte development / RNA methylation / corpus callosum development / rRNA base methylation / regulation of myelination / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of translation / cerebral cortex development / cognition ...rRNA (cytosine-C5-)-methyltransferase activity / oligodendrocyte development / RNA methylation / corpus callosum development / rRNA base methylation / regulation of myelination / Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of translation / cerebral cortex development / cognition / nucleolus / RNA binding / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Min, J.R. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The Crystal Structure of Human NSUN5 protein in complex with S-adenosyl-L-methionine Authors: Min, J.R. / Wu, H. / Zeng, H. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b9e.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b9e.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/2b9e ftp://data.pdbj.org/pub/pdb/validation_reports/b9/2b9e | HTTPS FTP |
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-Related structure data
Related structure data | 1ixkS 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: 33708.500 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: Q9NW70, UniProt: Q96P11*PLUS |
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#2: Chemical | ChemComp-SAM / |
#3: 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: 2.3 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: NSUN5 was complexed with S-adenosyl-L-methionine (SAM) (Sigma) at 1:10 molar ratio of protein :SAM and crystallized using the sitting drop vapor diffusion method at 20 C by mixing 1 l of the ...Details: NSUN5 was complexed with S-adenosyl-L-methionine (SAM) (Sigma) at 1:10 molar ratio of protein :SAM and crystallized using the sitting drop vapor diffusion method at 20 C by mixing 1 l of the protein solution with 1 l of the reservoir solution containing 10% Iso-propanole, 20% PEG 4000, 0.1M Na HEPES pH 7.5. , VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 4, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→59.55 Å / Num. all: 38415 / Num. obs: 38415 / % possible obs: 99.75 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.65→1.693 Å / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IXK Resolution: 1.65→59.55 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.638 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.097 / 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 mean: 22.801 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→59.55 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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