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Yorodumi- PDB-8crh: Crystal structure of Candida auris dihydrofolate reductase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8crh | ||||||
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Title | Crystal structure of Candida auris dihydrofolate reductase complexed with NADPH and cycloguanil | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | HYDROLASE / Dihydrofolate reductase candida auris NADPH cycloguanil | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / folic acid metabolic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | [Candida] auris (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Kirkman, T.J. / Dias, M.V.B. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Crystal structure of dihydrofolate reductase from the emerging pathogenic fungus Candida auris. Authors: Kirkman, T. / Sketcher, A. / de Morais Barroso, V. / Ishida, K. / Tosin, M. / Dias, M.V.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8crh.cif.gz | 217.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8crh.ent.gz | 173.4 KB | Display | PDB format |
PDBx/mmJSON format | 8crh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8crh_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8crh_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8crh_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 8crh_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8crh ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8crh | HTTPS FTP |
-Related structure data
Related structure data | 7zzxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24047.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) [Candida] auris (fungus) / Gene: QG37_02791 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L0P1H8 #2: Chemical | ChemComp-VIL / #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M Lithium sulphate, 0.1 M Tris, 27.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→42.36 Å / Num. obs: 112746 / % possible obs: 96.97 % / Redundancy: 11.6 % / Biso Wilson estimate: 16.11 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.01397 / Rrim(I) all: 0.05006 / Net I/σ(I): 19.59 |
Reflection shell | Resolution: 1.3→1.346 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4086 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9094 / CC1/2: 0.907 / CC star: 0.975 / Rpim(I) all: 0.2003 / Rrim(I) all: 0.458 / % possible all: 79.51 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→42.36 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→42.36 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: -16.6136 Å / Origin y: 10.4312 Å / Origin z: 52.5382 Å
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Refinement TLS group | Selection details: all |