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Open data
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Basic information
Entry | Database: PDB / ID: 3cr8 | ||||||
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Title | Hexameric APS kinase from Thiobacillus denitrificans | ||||||
![]() | Sulfate adenylyltransferase, adenylylsulfate kinase | ||||||
![]() | TRANSFERASE / APS kinase / Adenylylsulfate kinase / sulfate metabolism / Nucleotide 2 kinase / Nucleotidyltransferase | ||||||
Function / homology | ![]() adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / sulfate assimilation / hydrogen sulfide biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Gay, S.C. / Segel, I.H. / Fisher, A.J. | ||||||
![]() | ![]() Title: Structure of the two-domain hexameric APS kinase from Thiobacillus denitrificans: structural basis for the absence of ATP sulfurylase activity. Authors: Gay, S.C. / Segel, I.H. / Fisher, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291 KB | Display | ![]() |
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PDB format | ![]() | 234.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 467.5 KB | Display | ![]() |
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Full document | ![]() | 552.9 KB | Display | |
Data in XML | ![]() | 61.7 KB | Display | |
Data in CIF | ![]() | 83.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i2dS S: Starting model for refinement |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 61638.320 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q3SM86, sulfate adenylyltransferase, adenylyl-sulfate kinase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: K/Na Tartrate, NaCl, Bis Tris Propane, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2007 / Details: double crystal monochromator |
Radiation | Monochromator: Double Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. all: 3317 / Num. obs: 38467 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.107 / Χ2: 1.084 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 2.95→3.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.357 / Num. unique all: 3925 / Χ2: 0.818 / % possible all: 95.8 |
-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1I2D Resolution: 2.95→35.028 Å / Isotropic thermal model: isotropic / σ(F): 1.34 / 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: 19.07 Å2 / Biso mean: 60.52 Å2 / Biso min: 139.13 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→35.028 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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