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Yorodumi- PDB-7nu2: Crystal Structure of Neisseria gonorrhoeae LeuRS E169G mutant in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nu2 | ||||||||||||
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Title | Crystal Structure of Neisseria gonorrhoeae LeuRS E169G mutant in Complex with the Reaction Intermediate Leu-AMP | ||||||||||||
Components | Leucine--tRNA ligase | ||||||||||||
Keywords | LIGASE / protein-ligand complex / Rossmann fold / tRNA synthetase | ||||||||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||||||||
Authors | Pang, L. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: Commun Biol / Year: 2022 Title: Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip. Authors: Pang, L. / Zanki, V. / Strelkov, S.V. / Van Aerschot, A. / Gruic-Sovulj, I. / Weeks, S.D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nu2.cif.gz | 362.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nu2.ent.gz | 290.2 KB | Display | PDB format |
PDBx/mmJSON format | 7nu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/7nu2 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/7nu2 | HTTPS FTP |
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-Related structure data
Related structure data | 7ntyC 7ntzC 7nu0C 7nu1C 7nu3C 7nu4C 7nu5C 7nu6C 7nu7C 7nu8C 7nu9C 7nuaC 7nubC 7nucC 6q89S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 98113.281 Da / Num. of mol.: 1 / Fragment: Leucyl-tRNA Synthetase / Mutation: E169G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Strain: NCCP11945 / Gene: leuS, NGK_0009 / Plasmid: pETRUK / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) pLysS / References: UniProt: B4RNT1, leucine-tRNA ligase |
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-Non-polymers , 6 types, 387 molecules
#2: Chemical | #3: Chemical | ChemComp-ATP / | #4: Chemical | ChemComp-USB / [[( | #5: Chemical | ChemComp-ZN / | #6: Chemical | ChemComp-MG / | #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: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% (w/v) PEG 3350 and a crystal seed stock in a ...Details: Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 0.1 M bis-tris propane pH 8.5, 0.1 M MgCl2, 20% (w/v) PEG 3350 and a crystal seed stock in a 0.75:1.0:0.25 (v/v) ratio. The seed stock was prepared in the same crystallization buffer. Suitable crystals were soaked with 5 mM ATP and 5 mM L-leucine in an equilvalent precipitant solution supplemented with 22% (v/v) ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.918398 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 14, 2020 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918398 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.06→77.49 Å / Num. obs: 57491 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.038 / Rrim(I) all: 0.141 / Net I/σ(I): 12.4 / Num. measured all: 777663 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 100
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q89 Resolution: 2.1→77.49 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.59 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 145.13 Å2 / Biso mean: 49.7817 Å2 / Biso min: 20.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→77.49 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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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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