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Yorodumi- PDB-1g8h: ATP SULFURYLASE FROM S. CEREVISIAE: THE TERNARY PRODUCT COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g8h | ||||||
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Title | ATP SULFURYLASE FROM S. CEREVISIAE: THE TERNARY PRODUCT COMPLEX WITH APS AND PPI | ||||||
Components | SULFATE ADENYLYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / alpha-beta protein / beta-barrel / Rossmann-fold / kinase fold / product complex with adenosine-5'-phosphosulfate and pyrophosphate / displacement mechanism | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Ullrich, T.C. / Blaesse, M. / Huber, R. | ||||||
Citation | Journal: EMBO J. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g8h.cif.gz | 239.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g8h.ent.gz | 188.8 KB | Display | PDB format |
PDBx/mmJSON format | 1g8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g8/1g8h ftp://data.pdbj.org/pub/pdb/validation_reports/g8/1g8h | HTTPS FTP |
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-Related structure data
Related structure data | 1g8fSC 1g8gC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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. |
-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) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C-FY1679 / References: UniProt: P08536, sulfate adenylyltransferase |
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-Non-polymers , 8 types, 650 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.8 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 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: 2.8→25 Å / Num. all: 35298 / Num. obs: 35022 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.128 / Net I/σ(I): 5.8 |
Reflection shell | Resolution: 2.8→2.98 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 5600 / Rsym value: 0.457 / % possible all: 97.1 |
Reflection | *PLUS Rmerge(I) obs: 0.128 |
Reflection shell | *PLUS % possible obs: 97.1 % / Rmerge(I) obs: 0.428 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: residues 1-330 from 1G8F Resolution: 2.8→24.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4005513.35 / Data cutoff high rms absF: 4005513.35 / 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: 48.48 Å2 / ksol: 0.372 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.019 / 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: 35.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.332 / % reflection Rfree: 5 % / Rfactor Rwork: 0.254 |