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Yorodumi- PDB-5agj: Crystal structure of the LeuRS editing domain of Candida albicans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5agj | ||||||
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Title | Crystal structure of the LeuRS editing domain of Candida albicans in complex with the adduct AN2690-AMP | ||||||
Components | POTENTIAL CYTOSOLIC LEUCYL TRNA SYNTHETASE | ||||||
Keywords | LIGASE / AMINOACYL-TRNA SYNTHETASE / AMINOACYLATION / PROTEIN SYNTHESIS / PROOF-READING MECHANISMS / ANTIFUNGAL TARGET | ||||||
Function / homology | Isoleucyl-tRNA Synthetase; domain 2 / Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain / Alpha-Beta Complex / Alpha Beta / Chem-ANZ / : Function and homology information | ||||||
Biological species | CANDIDA ALBICANS (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zhao, H. / Palencia, A. / Seiradake, E. / Ghaemi, Z. / Luthey-Schulten, Z. / Cusack, S. / Martinis, S.A. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2015 Title: Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight Into the Leucyl-tRNA Synthetase Editing Mechanism. Authors: Zhao, H. / Palencia, A. / Seiradake, E. / Ghaemi, Z. / Cusack, S. / Luthey-Schulten, Z. / Martinis, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5agj.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5agj.ent.gz | 50.9 KB | Display | PDB format |
PDBx/mmJSON format | 5agj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5agj ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5agj | HTTPS FTP |
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-Related structure data
Related structure data | 5aghC 5agiC 2wfgS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 29497.600 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1), UNP RESIDUES 280-530 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CANDIDA ALBICANS (yeast) / Strain: SC5314 / Production host: ESCHERICHIA COLI K12 (bacteria) / Variant (production host): DH10B / References: UniProt: Q5A9A4, leucine-tRNA ligase |
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#2: Chemical | ChemComp-ANZ / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.39 % / Description: NONE |
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Crystal grow | pH: 7.4 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: ID23-2 / Wavelength: 0.8726 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 17, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.57 Å / Num. obs: 16451 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.73 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3.95 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WFG Resolution: 2→50.57 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.723 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.201 / ESU R Free: 0.178 / 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: 19.337 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50.57 Å
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Refine LS restraints |
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