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Yorodumi- PDB-5hvl: Structure of Candida albicans trehalose-6-phosphate synthase in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hvl | ||||||
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Title | Structure of Candida albicans trehalose-6-phosphate synthase in complex with UDP and validoxylamine A | ||||||
Components | Alpha,alpha-trehalose-phosphate synthase [UDP-forming] | ||||||
Keywords | TRANSFERASE / trehalose-6-phosphate synthase | ||||||
Function / homology | Function and homology information filamentous growth of a population of unicellular organisms in response to heat / filamentous growth of a population of unicellular organisms in response to biotic stimulus / cellular response to desiccation / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / trehalose metabolism in response to stress / filamentous growth ...filamentous growth of a population of unicellular organisms in response to heat / filamentous growth of a population of unicellular organisms in response to biotic stimulus / cellular response to desiccation / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose-phosphatase activity / trehalose biosynthetic process / trehalose metabolism in response to stress / filamentous growth / cellular response to heat / cytosol Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å | ||||||
Authors | Miao, Y. / Brennan, R.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: MBio / Year: 2017 Title: Structural and In Vivo Studies on Trehalose-6-Phosphate Synthase from Pathogenic Fungi Provide Insights into Its Catalytic Mechanism, Biological Necessity, and Potential for Novel Antifungal Drug Design. Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Maskarinec, S.A. / Liu, J. / Lee, R.E. / Perfect, J.R. / Brennan, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hvl.cif.gz | 219.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hvl.ent.gz | 173.1 KB | Display | PDB format |
PDBx/mmJSON format | 5hvl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hvl_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5hvl_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 5hvl_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 5hvl_validation.cif.gz | 63.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/5hvl ftp://data.pdbj.org/pub/pdb/validation_reports/hv/5hvl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 54521.172 Da / Num. of mol.: 2 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: TPS1, CaO19.13961, CaO19.6640 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: Q92410, alpha,alpha-trehalose-phosphate synthase (UDP-forming) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M lithium sulfate, 0.1 M Tris, 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 7, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 103765 / % possible obs: 99.6 % / Redundancy: 10.3 % / Biso Wilson estimate: 27.86 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.032 / Rrim(I) all: 0.098 / Χ2: 2.624 / Net I/av σ(I): 51.655 / Net I/σ(I): 11.1 / Num. measured all: 1073243 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Candida albicans Tps1 Resolution: 1.796→37.471 Å / FOM work R set: 0.8563 / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.74 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.54 Å2 / Biso mean: 31.99 Å2 / Biso min: 17.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.796→37.471 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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