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Yorodumi- PDB-8i1n: Crystal structure of APSK2 domain from human PAPSS2 in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 8i1n | ||||||
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Title | Crystal structure of APSK2 domain from human PAPSS2 in complex with endogenous APS and ADP | ||||||
Components | Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2 | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Adenosine 5'-phosphosulfate kinase domain 2 / APSK2 / human PAPSS2 | ||||||
Function / homology | Function and homology information Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process ...Defective PAPSS2 causes SEMD-PA / 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process / Transport and synthesis of PAPS / adenylyl-sulfate kinase / sulfate adenylyltransferase / adenylylsulfate kinase activity / sulfate adenylyltransferase (ATP) activity / Metabolism of ingested H2SeO4 and H2SeO3 into H2Se / sulfate assimilation / hormone metabolic process / nucleotidyltransferase activity / bone development / blood coagulation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Zhang, L. / Song, W.Y. / Zhang, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Structure / Year: 2023 Title: Redox switching mechanism of the adenosine 5'-phosphosulfate kinase domain (APSK2) of human PAPS synthase 2. Authors: Zhang, L. / Song, W. / Li, T. / Mu, Y. / Zhang, P. / Hu, J. / Lin, H. / Zhang, J. / Gao, H. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8i1n.cif.gz | 160.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8i1n.ent.gz | 129.7 KB | Display | PDB format |
PDBx/mmJSON format | 8i1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i1/8i1n ftp://data.pdbj.org/pub/pdb/validation_reports/i1/8i1n | HTTPS FTP |
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-Related structure data
Related structure data | 8i1mC 8i1oC 2ofxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 21809.680 Da / Num. of mol.: 4 / Fragment: APSK2 homodimer domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAPSS2, ATPSK2 / Production host: Escherichia coli (E. coli) References: UniProt: O95340, sulfate adenylyltransferase, adenylyl-sulfate kinase #2: Chemical | ChemComp-ADP / #3: Chemical | Has ligand of interest | Y | |
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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: 2.52 Å3/Da / Density % sol: 51.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.2 M Ammonium citrate dihydrate, pH7.0 and 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 5, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 21315 / % possible obs: 99 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.974 / Χ2: 0.097 / Net I/σ(I): 3.8 / Num. measured all: 132290 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OFX Resolution: 2.8→44.19 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.16 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→44.19 Å
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Refine LS restraints |
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LS refinement shell |
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