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- PDB-1hqo: CRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hqo | ||||||
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Title | CRYSTAL STRUCTURE OF THE NITROGEN REGULATION FRAGMENT OF THE YEAST PRION PROTEIN URE2P | ||||||
![]() | URE2 PROTEIN | ||||||
![]() | SIGNALING PROTEIN / glutathione S-transferase superfamily fold | ||||||
Function / homology | ![]() Oxidoreductases; Acting on a sulfur group of donors; With a disulfide as acceptor / protein urmylation / glutathione peroxidase / negative regulation of transcription by transcription factor localization / regulation of nitrogen utilization / glutathione peroxidase activity / nitrate assimilation / phosphoprotein binding / transcription corepressor activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Umland, T.C. / Taylor, K.L. / Rhee, S. / Wickner, R.B. / Davies, D.R. | ||||||
![]() | ![]() Title: The crystal structure of the nitrogen regulation fragment of the yeast prion protein Ure2p. Authors: Umland, T.C. / Taylor, K.L. / Rhee, S. / Wickner, R.B. / Davies, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.3 KB | Display | ![]() |
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PDB format | ![]() | 84.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.1 KB | Display | ![]() |
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Full document | ![]() | 452.9 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dimer. The dimer was contained within the asymmetric unit. |
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Components
#1: Protein | Mass: 29937.945 Da / Num. of mol.: 2 / Fragment: NITROGEN REGULATION FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: URE2 / Plasmid: PFLAG / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.84 % Description: The model was refined against the remote data set (0.9686 A). | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.8 Details: NaCl, Bicine, Tris-HCl, alpha-chymotrypsin, pH 8.8, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 2, 2000 | ||||||||||||
Radiation | Monochromator: Si monochomator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.3→20 Å / Num. all: 29499 / Num. obs: 168715 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 15.4 | ||||||||||||
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.32 / Num. unique all: 2941 / % possible all: 99.5 | ||||||||||||
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 29499 / Num. measured all: 168715 | ||||||||||||
Reflection shell | *PLUS % possible obs: 99.5 % / Rmerge(I) obs: 0.32 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 55.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Total num. of bins used: 10
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.221 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 55.6 Å2 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.3 Å / Rfactor Rfree: 0.358 / Rfactor Rwork: 0.315 |