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Open data
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Basic information
Entry | Database: PDB / ID: 1jv3 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN AGX1 COMPLEXED WITH UDPGALNAC | ||||||
![]() | GlcNAc1P uridyltransferase isoform 1: AGX1 | ||||||
![]() | TRANSFERASE / NUCLEOTIDYLTRANSFERASE / ALTERNATIVE SPLICING | ||||||
Function / homology | ![]() protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / antiviral innate immune response / positive regulation of type I interferon production ...protein serine pyrophosphorylase activity / UDP-N-acetylgalactosamine diphosphorylase / UDP-N-acetylgalactosamine diphosphorylase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a phosphate group as acceptor / Synthesis of UDP-N-acetyl-glucosamine / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / antiviral innate immune response / positive regulation of type I interferon production / nucleoplasm / identical protein binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Peneff, C. / Bourne, Y. | ||||||
![]() | ![]() Title: Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture. Authors: Peneff, C. / Ferrari, P. / Charrier, V. / Taburet, Y. / Monnier, C. / Zamboni, V. / Winter, J. / Harnois, M. / Fassy, F. / Bourne, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 218.7 KB | Display | ![]() |
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PDB format | ![]() | 173.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 64.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jv1SC ![]() 1jvdC ![]() 1jvgC 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 57095.965 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16222, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.24 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: peg600, Imidazole/malate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 5, 2001 |
Radiation | Monochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. all: 66084 / Num. obs: 64858 / % possible obs: 97.62 % / Observed criterion σ(I): 1.8 / Redundancy: 2.62 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.066 / Net I/σ(I): 7.4823 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 2.52 % / Mean I/σ(I) obs: 1.84 / Num. unique all: 5529 / Rsym value: 0.37 / % possible all: 98.18 |
Reflection | *PLUS % possible obs: 97.6 % / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: rigid body Starting model: pdb code: 1JV1 Resolution: 2.2→19.99 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1930205.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.1159 Å2 / ksol: 0.366139 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.189 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.281 / Rfactor Rwork: 0.232 |