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Yorodumi- PDB-3ziu: Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ziu | ||||||
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Title | Crystal structure of Mycoplasma mobile Leucyl-tRNA Synthetase with Leu-AMS in the active site | ||||||
Components | LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / ATP binding Similarity search - Function | ||||||
Biological species | MYCOPLASMA MOBILE (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Li, L. / Palencia, A. / Lukk, T. / Li, Z. / Luthey-Schulten, Z.A. / Cusack, S. / Martinis, S.A. / Boniecki, M.T. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Leucyl-tRNA Synthetase Editing Domain Functions as a Molecular Rheostat to Control Codon Ambiguity in Mycoplasma Pathogens. Authors: Li, L. / Palencia, A. / Lukk, T. / Li, Z. / Luthey-Schulten, Z.A. / Cusack, S. / Martinis, S.A. / Boniecki, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ziu.cif.gz | 281.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ziu.ent.gz | 227.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ziu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/3ziu ftp://data.pdbj.org/pub/pdb/validation_reports/zi/3ziu | HTTPS FTP |
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-Related structure data
Related structure data | 4aq7S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 75125.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 5-O-N-LEUCYL-SULFAMOYLADENOSINE, LEUCYL ADENYLATE ANALOGUE (LEUAMS) BOUND TO THE ACTIVE SITE Source: (gene. exp.) MYCOPLASMA MOBILE (bacteria) / Plasmid: P14LIMMOLEURS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q6KHA5, leucine-tRNA ligase #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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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: 2.82 Å3/Da / Density % sol: 56.46 % / Description: NONE |
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Crystal grow | pH: 5.5 Details: 0.1M BIS-TRIS PH 5.5 0.6M AMMONIUM ACETATE 20% V/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 4, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.07→12 Å / Num. obs: 101516 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.23 / Net I/σ(I): 18.45 |
Reflection shell | Resolution: 2.07→2.12 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2.56 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AQ7 Resolution: 2.07→135.76 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.485 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.711 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→135.76 Å
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Refine LS restraints |
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