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- PDB-4ypf: Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ypf | ||||||
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Title | Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with quinolin-3-amine (Chem 84) | ||||||
![]() | Histidyl-tRNA synthetase | ||||||
![]() | Ligase/Ligase inhibitor / ligase / aminoacyl-tRNA synthetase / aaRS / HisRS / Trypanosoma cruzi / protein-inhibitor complex / Ligase-Ligase inhibitor complex | ||||||
Function / homology | ![]() histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Koh, C.-Y. / Hol, W.G.J. | ||||||
![]() | ![]() Title: A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens. Authors: Koh, C.Y. / Siddaramaiah, L.K. / Ranade, R.M. / Nguyen, J. / Jian, T. / Zhang, Z. / Gillespie, J.R. / Buckner, F.S. / Verlinde, C.L. / Fan, E. / Hol, W.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 180.4 KB | Display | ![]() |
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PDB format | ![]() | 139.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yp0C ![]() 4yrcC ![]() 4yreC ![]() 4yrfC ![]() 4yrgC ![]() 4yriC ![]() 4yrjC ![]() 4yrkC ![]() 4yrlC ![]() 4yrmC ![]() 4yrnC ![]() 4yroC ![]() 4yrpC ![]() 4yrqC ![]() 4yrrC ![]() 4yrsC ![]() 4yrtC ![]() 3lc0S 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: 51185.590 Da / Num. of mol.: 1 / Fragment: UNP residues 45-478 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: CL Brener / Gene: Tc00.1047053507019.40 / Plasmid: AVA0421 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 103 molecules ![](data/chem/img/HIS.gif)
![](data/chem/img/4FS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/4FS.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/DMS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HIS / | ||||
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#3: Chemical | ChemComp-4FS / | ||||
#4: Chemical | ChemComp-EDO / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP PH range: 4.8 to 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 28, 2013 | |||||||||||||||||||||||||||
Radiation | Monochromator: VariMax HF (Osmic) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.2→36 Å / Num. obs: 24924 / % possible obs: 98.4 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.041 / Net I/σ(I): 15.1 / Num. measured all: 72379 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3LC0 Resolution: 2.2→36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.573 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.251 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 127.27 Å2 / Biso mean: 54.029 Å2 / Biso min: 22.39 Å2
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Refinement step | Cycle: final / Resolution: 2.2→36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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