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Yorodumi- PDB-5dxo: Structure of Aspergillus fumigatus trehalose-6-phosphate phosphat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5dxo | ||||||
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Title | Structure of Aspergillus fumigatus trehalose-6-phosphate phosphatase crystal form 3 | ||||||
Components | trehalose-6-phosphate phosphatase | ||||||
Keywords | HYDROLASE / trehalose-6-phosphate / phosphatase | ||||||
Function / homology | Function and homology information asexual sporulation resulting in formation of a cellular spore / hyphal growth / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / trehalose-phosphatase activity / trehalose biosynthetic process / fungal-type cell wall organization / positive regulation of autophagy ...asexual sporulation resulting in formation of a cellular spore / hyphal growth / alpha,alpha-trehalose-phosphate synthase (UDP-forming) / alpha,alpha-trehalose-phosphate synthase (UDP-forming) activity / alpha,alpha-trehalose-phosphate synthase complex (UDP-forming) / trehalose metabolism in response to stress / trehalose-phosphatase activity / trehalose biosynthetic process / fungal-type cell wall organization / positive regulation of autophagy / cellular response to heat / metal ion binding Similarity search - Function | ||||||
Biological species | Neosartorya fumigata (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Miao, Y. / Brennan, R.G. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Structures of trehalose-6-phosphate phosphatase from pathogenic fungi reveal the mechanisms of substrate recognition and catalysis. Authors: Miao, Y. / Tenor, J.L. / Toffaletti, D.L. / Washington, E.J. / Liu, J. / Shadrick, W.R. / Schumacher, M.A. / 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 | 5dxo.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dxo.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 5dxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dxo_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 5dxo_full_validation.pdf.gz | 443.6 KB | Display | |
Data in XML | 5dxo_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 5dxo_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/5dxo ftp://data.pdbj.org/pub/pdb/validation_reports/dx/5dxo | HTTPS FTP |
-Related structure data
Related structure data | 5dx9C 5dxfC 5dxiC 5dxlSC 5dxnC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 32675.988 Da / Num. of mol.: 2 / Fragment: UNP residues 674-949 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (mold) / Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_3G05650 / Production host: Escherichia coli (E. coli) References: UniProt: Q4WWF5, alpha,alpha-trehalose-phosphate synthase (UDP-forming) #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 44.2 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, 12% PEG3350 |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 44707 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 39.33 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Rrim(I) all: 0.082 / Χ2: 1.83 / Net I/av σ(I): 27.877 / Net I/σ(I): 12.7 / Num. measured all: 166375 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PDB entry 5DXL Resolution: 1.9→31.768 Å / FOM work R set: 0.7662 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.84 / 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: 108.05 Å2 / Biso mean: 45.7 Å2 / Biso min: 20 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→31.768 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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