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Yorodumi- PDB-5agh: Crystal structure of the LeuRS editing domain of Candida albicans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5agh | ||||||
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Title | Crystal structure of the LeuRS editing domain of Candida albicans Mutant K510A | ||||||
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 / ACETATE ION / : Function and homology information | ||||||
Biological species | CANDIDA ALBICANS (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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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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 | 5agh.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5agh.ent.gz | 48.4 KB | Display | PDB format |
PDBx/mmJSON format | 5agh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5agh_validation.pdf.gz | 438.4 KB | Display | wwPDB validaton report |
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Full document | 5agh_full_validation.pdf.gz | 439.2 KB | Display | |
Data in XML | 5agh_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 5agh_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/5agh ftp://data.pdbj.org/pub/pdb/validation_reports/ag/5agh | HTTPS FTP |
-Related structure data
Related structure data | 5agiC 5agjC 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: 29439.432 Da / Num. of mol.: 1 / Fragment: EDITING DOMAIN (CP1), UNP RESIDUES 280-530 / Mutation: YES 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 | #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: 2.01 Å3/Da / Density % sol: 38.75 % / Description: NONE |
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Crystal grow | pH: 4 Details: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 4.0, 24% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→64 Å / Num. obs: 18976 / % possible obs: 90.5 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 1.81→1.85 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.6 / % possible all: 49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WFG Resolution: 1.81→64.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.045 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 27.545 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→64.42 Å
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Refine LS restraints |
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