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Yorodumi- PDB-3uie: Crystal structure of adenosine 5'-phosphosulfate kinase from Arab... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uie | ||||||
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Title | Crystal structure of adenosine 5'-phosphosulfate kinase from Arabidopsis Thaliana in Complex with AMPPNP and APS | ||||||
Components | Adenylyl-sulfate kinase 1, chloroplastic | ||||||
Keywords | transferase/transferase inhibitor / Rossmann fold / Kinase / chloroplast / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information adenylyl-sulfate kinase / adenylylsulfate kinase activity / sulfate assimilation / hydrogen sulfide biosynthetic process / cysteine biosynthetic process / plastid / chloroplast / phosphorylation / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å | ||||||
Authors | Ravilious, G.E. / Jez, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural basis and evolution of redox regulation in plant adenosine-5'-phosphosulfate kinase. Authors: Ravilious, G.E. / Nguyen, A. / Francois, J.A. / Jez, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uie.cif.gz | 248 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uie.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 3uie.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/3uie ftp://data.pdbj.org/pub/pdb/validation_reports/ui/3uie | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Chain A and symmetry mate form crystallographic dimer Chain B and C form non-crystallographic dimer |
-Components
#1: Protein | Mass: 22104.318 Da / Num. of mol.: 3 / Fragment: UNP residues 77-276 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AKN1, At2g14750, F26C24.11, T6B13.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q43295, adenylyl-sulfate kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: 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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 200 mM magnesium chloride, 17.5 % PEG 2000, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2010 |
Radiation | Monochromator: high resolution double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.794→30.5 Å / Num. all: 70893 / Num. obs: 69476 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.8→1.83 Å / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.794→30.5 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 22.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.739 Å2 / ksol: 0.416 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.794→30.5 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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