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- PDB-7fha: Crystal structure of the ATP sulfurylase domain of human PAPSS2 i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7fha | ||||||||||||
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Title | Crystal structure of the ATP sulfurylase domain of human PAPSS2 in complex with APS | ||||||||||||
![]() | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | ||||||||||||
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Function / homology | ![]() Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Zhang, P. / Zhang, L. / Zhang, L. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for the substrate recognition mechanism of ATP-sulfurylase domain of human PAPS synthase 2. Authors: Zhang, P. / Zhang, L. / Hou, Z. / Lin, H. / Gao, H. / Zhang, 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 | ![]() | 194 KB | Display | ![]() |
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PDB format | ![]() | 149.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7fh3C ![]() 1x6vS 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
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/BGC.gif)
![](data/chem/img/BGC.gif)
#1: Protein | Mass: 45018.793 Da / Num. of mol.: 2 / Fragment: Sulfate adenylyltransferase,ATP sulfurylase Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: O95340, ![]() ![]() #3: Sugar | ![]() |
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-Non-polymers , 4 types, 858 molecules ![](data/chem/img/ADX.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #4: Chemical | #5: Chemical | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.07 Å3/Da / Density % sol: 59.99 % |
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Crystal grow![]() | Temperature: 277 K / Method: evaporation / Details: 0.1M HEPES, pH7.5, 25% PEG 3350 |
-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: Jul 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→50 Å / Num. obs: 75483 / % possible obs: 99.66 % / Redundancy: 12.6 % / CC1/2: 0.973 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 2→2.07 Å / Num. unique obs: 7394 / CC1/2: 0.973 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1X6V Resolution: 2→47.18 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 15.91 / 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: 99.42 Å2 / Biso mean: 27.7116 Å2 / Biso min: 11.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→47.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28
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