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Yorodumi- PDB-7rh8: Crystal structure of Fur1p from Candida albicans, in complex with UTP -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rh8 | ||||||
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Title | Crystal structure of Fur1p from Candida albicans, in complex with UTP | ||||||
Components | Uracil phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / fur1 / drug target / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / national institute of allergy and infectious diseases | ||||||
Function / homology | xenobiotic metabolic process => GO:0006805 / pyrimidine-containing compound salvage / cellular response to xenobiotic stimulus => GO:0071466 / uracil phosphoribosyltransferase activity / nucleoside metabolic process / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / URIDINE 5'-TRIPHOSPHATE / Uracil phosphoribosyltransferase Function and homology information | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Stogios, P.J. / Skarina, T. / Kim, Y. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Fur1p from Candida albicans, in complex with UTP Authors: Stogios, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rh8.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rh8.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 7rh8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/7rh8 ftp://data.pdbj.org/pub/pdb/validation_reports/rh/7rh8 | HTTPS FTP |
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-Related structure data
Related structure data | 1jlsS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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
#1: Protein | Mass: 24506.744 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: FUR1, orf19.2640, CAALFM_C503390CA / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Gold / References: UniProt: Q59QT3 |
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#2: Chemical | ChemComp-UTP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.57 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 25% (w/v) PEG3350, 0.2 M NaCl, 0.1 M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97869 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97869 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. obs: 35544 / % possible obs: 98 % / Redundancy: 13.4 % / Biso Wilson estimate: 22 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.022 / Net I/σ(I): 29.73 |
Reflection shell | Resolution: 1.7→1.73 Å / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1496 / CC1/2: 0.949 / Rpim(I) all: 0.262 / % possible all: 84.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JLS Resolution: 1.69→47.78 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.381 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→47.78 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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