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Yorodumi- PDB-6dep: Crystal structure of Candida albicans acetohydroxyacid synthase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dep | ||||||
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Title | Crystal structure of Candida albicans acetohydroxyacid synthase in complex with the herbicide sulfometuron methyl | ||||||
Components | Acetolactate synthase | ||||||
Keywords | transferase/transferase inhibitor / AHAS / acetohydroxyacid synthase / acetolactate synthase / herbicide / thiamin diphosphate / FAD / transferase / sulfometuron methyl / sulfonylurea / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information acetolactate synthase / acetolactate synthase complex / acetolactate synthase activity / valine biosynthetic process / isoleucine biosynthetic process / thiamine pyrophosphate binding / amino acid biosynthetic process / flavin adenine dinucleotide binding / magnesium ion binding / mitochondrion Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å | ||||||
Authors | Garcia, M.D. / Guddat, L.W. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Commercial AHAS-inhibiting herbicides are promising drug leads for the treatment of human fungal pathogenic infections. Authors: Garcia, M.D. / Chua, S.M.H. / Low, Y.S. / Lee, Y.T. / Agnew-Francis, K. / Wang, J.G. / Nouwens, A. / Lonhienne, T. / Williams, C.M. / Fraser, J.A. / Guddat, L.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dep.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dep.ent.gz | 225 KB | Display | PDB format |
PDBx/mmJSON format | 6dep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/de/6dep ftp://data.pdbj.org/pub/pdb/validation_reports/de/6dep | HTTPS FTP |
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-Related structure data
Related structure data | 6dekSC 6delC 6demC 6denC 6deoC 6deqC 6derC 6desC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74315.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast) Strain: SC5314 / ATCC MYA-2876 / Gene: ILV2, orf19.1613, CAALFM_C302320WA / Plasmid: pET30a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D8PJF9, acetolactate synthase |
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-Non-polymers , 7 types, 638 molecules
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-1SM / |
#6: Chemical | ChemComp-TZD / |
#7: Chemical | ChemComp-TP9 / ( |
#8: 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: 5.37 Å3/Da / Density % sol: 77 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 1 mM FAD, 1 mM ThDP, 5 mM MgCl2, 5 mM DTT, 3 mM sodium pyruvate, 1 M Na/K tartrate, 0.1 M CHES, and 0.2 M ammonium sulfate, 1 mM sulfometuron methyl PH range: 9.4-9.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 23, 2016 |
Radiation | Monochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.149→48.26 Å / Num. obs: 87576 / % possible obs: 99.7 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.058 / Rrim(I) all: 0.145 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.149→2.19 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4151 / Rpim(I) all: 0.29 / Rrim(I) all: 0.717 / % possible all: 94.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DEK Resolution: 2.149→46.647 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.82
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.149→46.647 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 20.1725 Å / Origin y: 80.4359 Å / Origin z: 75.6768 Å
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Refinement TLS group | Selection details: all |