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Yorodumi- PDB-7yp8: Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leuc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yp8 | ||||||||||||
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Title | Neisseria gonorrhoeae Leucyl-tRNA Synthetase in Complex with Leucyl-sulfamoyl 3-deazaadenosine | ||||||||||||
Components | Leucine--tRNA ligase | ||||||||||||
Keywords | LIGASE / protein-inhibitor 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. / De Graef, S. / Strelkov, S.V. / Weeks, S.D. | ||||||||||||
Funding support | Belgium, 3items
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Citation | Journal: To be published Title: The essential role of a structured water in base recognition of Class II aminoacyl-tRNA synthetases Authors: Pang, L. / De Graef, S. / Zhang, B. / Strelkov, S.V. / Van Aerschot, A. / 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 | 7yp8.cif.gz | 355 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yp8.ent.gz | 284.8 KB | Display | PDB format |
PDBx/mmJSON format | 7yp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7yp8 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7yp8 | HTTPS FTP |
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-Related structure data
Related structure data | 6q89S S: Starting model for refinement |
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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: 98185.344 Da / Num. of mol.: 1 / Mutation: D454N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria) 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 , 5 types, 329 molecules
#2: Chemical | ChemComp-EDO / |
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#3: Chemical | ChemComp-JIE / [( Mass: 458.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H26N6O7S / Feature type: SUBJECT OF INVESTIGATION |
#4: Chemical | ChemComp-ZN / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-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: 2.36 Å3/Da / Density % sol: 47.96 % / Mosaicity: 0.22 ° |
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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 0. ...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 2 mM synthesized inhibitor 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: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 15, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.09→82.98 Å / Num. obs: 56718 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.034 / Rrim(I) all: 0.094 / Net I/σ(I): 12.9 / Num. measured all: 424072 / Scaling rejects: 5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q89 Resolution: 2.1→56.21 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 22.56 / 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: 136.75 Å2 / Biso mean: 52.716 Å2 / Biso min: 25.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→56.21 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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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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