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- PDB-1g8g: ATP SULFURYLASE FROM S. CEREVISIAE: THE BINARY PRODUCT COMPLEX WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1g8g | ||||||
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Title | ATP SULFURYLASE FROM S. CEREVISIAE: THE BINARY PRODUCT COMPLEX WITH APS | ||||||
![]() | SULFATE ADENYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / alpha-beta protein / beta-barrel / Rossmann-fold / kinase fold / product complex with adenosine-5'-phosphosulfate / displacement mechanism | ||||||
Function / homology | ![]() sulfur amino acid metabolic process / sulfate assimilation via adenylyl sulfate reduction / sulfate assimilation, phosphoadenylyl sulfate reduction by phosphoadenylyl-sulfate reductase (thioredoxin) / sulfate adenylyltransferase / sulfate adenylyltransferase (ATP) activity / hydrogen sulfide biosynthetic process / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ullrich, T.C. / Blaesse, M. / Huber, R. | ||||||
![]() | ![]() Title: Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation. Authors: Ullrich, T.C. / Blaesse, M. / Huber, 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 | ![]() | 245.6 KB | Display | ![]() |
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PDB format | ![]() | 192.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 50.4 KB | Display | |
Data in CIF | ![]() | 73.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g8fSC ![]() 1g8hC 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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1 | ![]()
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Unit cell |
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Details | The biological assembly is a homo-hexamer: Each of the two crystallograhic independent subunits in the asymmtric unit create one trimer ring (D3 assembly). Two rings assemble in a staggered conformation. |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 57821.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NATIVE PURIFICATION OUT OF YEAST CELLS! / Source: (natural) ![]() ![]() |
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-Non-polymers , 8 types, 813 molecules ![](data/chem/img/CD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADX.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/ADX.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-NA / #5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-ACY / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.74 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 500 mM Sodium acetate, 50 mM HEPES, 25 mM Cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 2000 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. all: 45468 / Num. obs: 45307 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6 % / Biso Wilson estimate: 35 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6950 / Rsym value: 0.413 / % possible all: 97.3 |
Reflection | *PLUS Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 97.3 % / Rmerge(I) obs: 0.413 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: residues 1-330 from 1G8F Resolution: 2.6→24.85 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3960150.63 / Data cutoff high rms absF: 3960150.63 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.85 Å2 / ksol: 0.378 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→24.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.9 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.275 / % reflection Rfree: 5.1 % / Rfactor Rwork: 0.222 |