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Yorodumi- PDB-2wfg: Structure of the Candida albicans cytosolic leucyl-tRNA synthetas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wfg | ||||||
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Title | Structure of the Candida albicans cytosolic leucyl-tRNA synthetase editing domain bound to a benzoxaborole-AMP adduct | ||||||
Components | CYTOSOLIC LEUCYL-TRNA SYNTHETASE | ||||||
Keywords | LIGASE / LEUCYL-TRNA SYNTHETASE / EDITING DOMAIN / CANDIDA ALBICANS / HYDROLYSIS OF MIS-CHARGED TRNAS / BENZOXABOROLE / ANTI-FUNGAL | ||||||
Function / homology | Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Alpha-Beta Complex / Alpha Beta / Chem-ZZB / : Function and homology information | ||||||
Biological species | CANDIDA ALBICANS (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Seiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal Structures of the Human and Fungal Cytosolic Leucyl-tRNA Synthetase Editing Domains: A Structural Basis for the Rational Design of Antifungal Benzoxaboroles. Authors: Seiradake, E. / Mao, W. / Hernandez, V. / Baker, S.J. / Plattner, J.J. / Alley, M.R.K. / Cusack, S. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wfg.cif.gz | 113.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wfg.ent.gz | 92.7 KB | Display | PDB format |
PDBx/mmJSON format | 2wfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wf/2wfg ftp://data.pdbj.org/pub/pdb/validation_reports/wf/2wfg | HTTPS FTP |
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-Related 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: 29496.615 Da / Num. of mol.: 1 / Fragment: EDITING OR CP1 DOMAIN, RESIDUES 280-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DH10B / Variant (production host): 10G / References: UniProt: Q5A9A4 |
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#2: Chemical | ChemComp-ZZB / [( |
#3: Water | ChemComp-HOH / |
Nonpolymer details | AN3018-AMP ADDUCT (ZZB): AN3018 IS 6-ETHYLAMINO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 41.1 % / Description: NONE |
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Crystal grow | Details: 0.2 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 12930 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.16 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.31 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.26 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.88 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.883 / SU B: 16.747 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 22.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.88 Å
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Refine LS restraints |
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