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- PDB-7dsj: Anthranilate phosphoribosyltransferase from Saccharomyces cerevis... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dsj | |||||||||
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Title | Anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae in complex with PRPP and Mg | |||||||||
![]() | Anthranilate phosphoribosyltransferase | |||||||||
![]() | TRANSFERASE / Glycosyltransferase / Tryptophan biosynthesis | |||||||||
Function / homology | ![]() anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wu, X. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of anthranilate phosphoribosyltransferase from Saccharomyces cerevisiae. Authors: Wu, X. / Zhang, M. / Kuang, Z. / Yue, J. / Xue, L. / Zhu, M. / Zhu, Z. / Khan, M.H. / Niu, L. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.4 KB | Display | ![]() |
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PDB format | ![]() | 118.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 27.9 KB | Display | |
Data in CIF | ![]() | 38.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dsmSC ![]() 7dsoC ![]() 7dspC ![]() 7dsrC S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 41701.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P07285, anthranilate phosphoribosyltransferase #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.62 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M BIS-TRIS PH 6.5, 16% W/V PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.44→50 Å / Num. obs: 29444 / % possible obs: 100 % / Redundancy: 13.1 % / Rpim(I) all: 0.027 / Rrim(I) all: 0.097 / Net I/σ(I): 24.3 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 12.9 % / Mean I/σ(I) obs: 4 / Num. unique obs: 1440 / Rpim(I) all: 0.134 / Rrim(I) all: 0.484 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DSM Resolution: 2.44→46.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.965 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.468 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.56 Å2 / Biso mean: 41.681 Å2 / Biso min: 23.53 Å2
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Refinement step | Cycle: final / Resolution: 2.44→46.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.44→2.502 Å / Rfactor Rfree error: 0
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