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Open data
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Basic information
Entry | Database: PDB / ID: 4p74 | ||||||
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Title | PheRS in complex with compound 3a | ||||||
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![]() | LIGASE/LIGASE INHIBITOR / Phenylalanine tRNA synthetase / PheRS / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | ![]() phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / tRNA binding / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ferguson, A.D. | ||||||
![]() | ![]() Title: The role of a novel auxiliary pocket in bacterial phenylalanyl-tRNA synthetase druggability. Authors: Abibi, A. / Ferguson, A.D. / Fleming, P.R. / Gao, N. / Hajec, L.I. / Hu, J. / Laganas, V.A. / McKinney, D.C. / McLeod, S.M. / Prince, D.B. / Shapiro, A.B. / Buurman, E.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 791.9 KB | Display | ![]() |
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PDB format | ![]() | 659.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4p71SC ![]() 4p72C ![]() 4p73C ![]() 4p75C 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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Unit cell |
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Components
#1: Protein | Mass: 86902.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 38111.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 18% PEG 3350, 0.2M ammonium citrate tri-basic (pH 6.2) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→61 Å / Num. obs: 69943 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 66.15 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4p71 Resolution: 2.7→60.98 Å / Cor.coef. Fo:Fc: 0.9327 / Cor.coef. Fo:Fc free: 0.9178 / SU R Cruickshank DPI: 0.882 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.652 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.282
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Displacement parameters | Biso mean: 60.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.365 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→60.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 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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