+Open data
-Basic information
Entry | Database: PDB / ID: 6ajk | ||||||||||||
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Title | Crystal structure of TFB1M and h45 in homo sapiens | ||||||||||||
Components |
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Keywords | TRANSFERASE/RNA / TFB1M / helix45 / TRANSFERASE-RNA complex | ||||||||||||
Function / homology | Function and homology information rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / mitochondrial matrix ...rRNA modification in the mitochondrion / mitochondrial transcription factor activity / transcription initiation at mitochondrial promoter / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA modification / rRNA methylation / mitochondrial nucleoid / Transferases; Transferring one-carbon groups; Methyltransferases / Transcriptional activation of mitochondrial biogenesis / mitochondrial matrix / DNA binding / RNA binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å | ||||||||||||
Authors | Liu, X. / Shen, S. / Wu, P. / Li, F. / Wang, C. / Gong, Q. / Wu, J. / Zhang, H. / Shi, Y. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structural insights into dimethylation of 12S rRNA by TFB1M: indispensable role in translation of mitochondrial genes and mitochondrial function. Authors: Liu, X. / Shen, S. / Wu, P. / Li, F. / Liu, X. / Wang, C. / Gong, Q. / Wu, J. / Yao, X. / Zhang, H. / Shi, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ajk.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ajk.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ajk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/6ajk ftp://data.pdbj.org/pub/pdb/validation_reports/aj/6ajk | HTTPS FTP |
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-Related structure data
Related structure data | 6aasC 6aauC 6aaxC 4gc5S 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: 36753.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TFB1M, CGI-75 / Production host: Escherichia coli (E. coli) References: UniProt: Q8WVM0, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: RNA chain | Mass: 9035.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1M sodium citrate, pH 5.0, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3→40 Å / Num. obs: 11458 / % possible obs: 98.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 30.25 Å2 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.101 / Rrim(I) all: 0.273 / Χ2: 0.46 / Net I/σ(I): 2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4GC5 Resolution: 3.001→37.271 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 20.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.61 Å2 / Biso mean: 24.7873 Å2 / Biso min: 10.31 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.001→37.271 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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