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Yorodumi- PDB-8vc5: Crystal structure of glutamyl-tRNA synthetase GluRS from Pseudomo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vc5 | |||||||||
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Title | Crystal structure of glutamyl-tRNA synthetase GluRS from Pseudomonas aeruginosa (Zinc bound) | |||||||||
Components | Glutamate--tRNA ligase | |||||||||
Keywords | LIGASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / GLUTAMATE--TRNA LIGASE | |||||||||
Function / homology | Function and homology information glutamate-tRNA ligase / glutamate-tRNA ligase activity / glutamyl-tRNA aminoacylation / tRNA binding / zinc ion binding / ATP binding / cytosol Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 2items
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Citation | Journal: To be published Title: Crystal structure of glutamyl-tRNA synthetase GluRS from Pseudomonas aeruginosa (Zinc bound) Authors: Seibold, S. / Lovell, S. / Battaile, K.P. / Fenwick, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vc5.cif.gz | 398.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vc5.ent.gz | 325.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/8vc5 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vc5 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57857.371 Da / Num. of mol.: 2 / Fragment: PsaeA.01348.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: gltX, PA3134 / Plasmid: PsaeA.01348.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9XCL6, glutamate-tRNA ligase |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-2PE / | #6: Chemical | ChemComp-GOL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Berkeley D8: 20% (w/v) PEG 3350, 100 mM MES / Sodium hydroxide pH 5.5, 100 mM Ammonium citrate dibasic, 5% (v/v) 2-Propanol. PsaeA.01348.a.B1.PW37887 at 46 mg/mL. plate 13731 well D8 drop 3. ...Details: Berkeley D8: 20% (w/v) PEG 3350, 100 mM MES / Sodium hydroxide pH 5.5, 100 mM Ammonium citrate dibasic, 5% (v/v) 2-Propanol. PsaeA.01348.a.B1.PW37887 at 46 mg/mL. plate 13731 well D8 drop 3. Puck: PSL-1902, Cryo: 80% crystallant + 20% ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 24, 2023 |
Radiation | Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→46.81 Å / Num. obs: 52286 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.031 / Rrim(I) all: 0.099 / Χ2: 0.98 / Net I/σ(I): 14.3 / Num. measured all: 528827 |
Reflection shell | Resolution: 2.3→2.37 Å / % possible obs: 100 % / Redundancy: 9.7 % / Rmerge(I) obs: 1.341 / Num. measured all: 43283 / Num. unique obs: 4476 / CC1/2: 0.795 / Rpim(I) all: 0.444 / Rrim(I) all: 1.414 / Χ2: 0.97 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→45.33 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.33 Å
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Refine LS restraints |
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LS refinement shell |
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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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