+Open data
-Basic information
Entry | Database: PDB / ID: 4p72 | ||||||
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Title | PheRS in complex with compound 2a | ||||||
Components |
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Keywords | LIGASE/LIGASE INHIBITOR / Phenylalanine tRNA synthetase / PheRS / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å | ||||||
Authors | Ferguson, A.D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p72.cif.gz | 790.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p72.ent.gz | 655.9 KB | Display | PDB format |
PDBx/mmJSON format | 4p72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p72_validation.pdf.gz | 696.7 KB | Display | wwPDB validaton report |
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Full document | 4p72_full_validation.pdf.gz | 723.9 KB | Display | |
Data in XML | 4p72_validation.xml.gz | 68 KB | Display | |
Data in CIF | 4p72_validation.cif.gz | 93.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p7/4p72 ftp://data.pdbj.org/pub/pdb/validation_reports/p7/4p72 | HTTPS FTP |
-Related structure data
Related structure data | 4p71SC 4p73C 4p74C 4p75C 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: 86902.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pheT, PA2739 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0A4, phenylalanine-tRNA ligase #2: Protein | Mass: 38111.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pheS, PA2740 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I0A3, phenylalanine-tRNA ligase #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 56.97 % |
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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 tr-basic (pH 6.2) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Mar 19, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.62→75.87 Å / Num. obs: 76043 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 63.16 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.62→2.69 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4p71 Resolution: 2.62→75.87 Å / Cor.coef. Fo:Fc: 0.9369 / Cor.coef. Fo:Fc free: 0.9098 / SU R Cruickshank DPI: 0.577 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.482 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.267
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Displacement parameters | Biso mean: 54.62 Å2
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Refine analyze | Luzzati coordinate error obs: 0.349 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.62→75.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.69 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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