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- PDB-6hhz: Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6hhz | ||||||||||||
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Title | Klebsiella pneumoniae Seryl-tRNA Synthetase in Complex with 5'-O-(N-(L-seryl)-sulfamoyl)cytidine | ||||||||||||
![]() | Serine--tRNA ligase | ||||||||||||
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Function / homology | ![]() selenocysteine biosynthetic process / seryl-tRNA aminoacylation / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Pang, L. / De Graef, S. / Weeks, S.D. / Strelkov, S.V. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Insights into the Binding of Natural Pyrimidine-Based Inhibitors of Class II Aminoacyl-tRNA Synthetases. Authors: Pang, L. / Nautiyal, M. / De Graef, S. / Gadakh, B. / Zorzini, V. / Economou, A. / Strelkov, S.V. / Van Aerschot, A. / Weeks, S.D. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.7 KB | Display | ![]() |
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PDB format | ![]() | 146.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6hdzC ![]() 6he1C ![]() 6he3C ![]() 6hhvC ![]() 6hhwC ![]() 6hhxC ![]() 6hhyC ![]() 6hi0C ![]() 6rltC ![]() 6rluC ![]() 6rlvC ![]() 6s30C ![]() 6sjcC ![]() 2dq3S C: citing same article ( S: Starting model for refinement |
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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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 48669.180 Da / Num. of mol.: 1 / Fragment: Seryl-tRNA synthetase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 190 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/FZQ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FZQ.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-FZQ / | #4: Chemical | #5: Chemical | ChemComp-CL / | ![]() #6: Chemical | ChemComp-1PE / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.94 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus ...Details: Holo protein, concentrated to 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 5 mM DTT, was mixed with an equal volume of 7.5% w/v PEG 8000, 50 mM CaCl2, 20% v/v ethylene glycol, 100 mM Morpheus buffer system 1 (MES/Imidazole) pH 6.5. Suitable crystals were soaked with 2 mM compound in a similar crystallization solution containing a 10% w/v PEG 8000. |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||
Reflection | Resolution: 1.93→114.66 Å / Num. obs: 61829 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 50.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.1 / Net I/σ(I): 10.7 / Num. measured all: 523095 / Scaling rejects: 1 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.8
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: Model generated from structure 2DQ3 Resolution: 2.15→43 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU R Cruickshank DPI: 0.146 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.151 / SU Rfree Blow DPI: 0.139 / SU Rfree Cruickshank DPI: 0.137
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Displacement parameters | Biso max: 158.34 Å2 / Biso mean: 55.1 Å2 / Biso min: 32.14 Å2
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Refine analyze | Luzzati coordinate error obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→43 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.21 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -11.7862 Å / Origin y: -31.1086 Å / Origin z: -9.6704 Å
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Refinement TLS group | Selection details: {A|*} |