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Open data
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Basic information
Entry | Database: PDB / ID: 6qkv | |||||||||
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Title | Structure of YibK from P. aeruginosa | |||||||||
![]() | tRNA (cytidine(34)-2'-O)-methyltransferase | |||||||||
![]() | TRANSFERASE / methyltransferase | |||||||||
Function / homology | ![]() wobble position cytosine ribose methylation / wobble position uridine ribose methylation / tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mikula, K.M. / Tascon, I. / Iwai, H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Tying up the Loose Ends: A Mathematically Knotted Protein. Authors: Hsu, S.D. / Lee, Y.C. / Mikula, K.M. / Backlund, S.M. / Tascon, I. / Goldman, A. / Iwai, H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 56.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6qh8C ![]() 1mxiS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17706.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trmL, C0044_37955, C8257_31370, DZ962_17365, PAMH19_2880 Production host: ![]() ![]() References: UniProt: A0A071LCY6, UniProt: Q9HU57*PLUS, tRNA (cytidine34-2'-O)-methyltransferase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.15 M ammonium sulfate, 0.9 M lithium sulfate, 0.1 M sodium citrate buffer, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 14, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→46.7 Å / Num. obs: 23919 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rrim(I) all: 0.071 / Net I/σ(I): 18.52 |
Reflection shell | Resolution: 2.01→2.13 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 2.84 / Num. unique obs: 3813 / Rrim(I) all: 0.665 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1mxi Resolution: 2.01→46.699 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.45
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.01→46.699 Å
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Refine LS restraints |
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LS refinement shell |
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