+Open data
-Basic information
Entry | Database: PDB / ID: 1jv1 | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN AGX1 COMPLEXED WITH UDPGLCNAC | ||||||
Components | GlcNAc1P uridyltransferase isoform 1: AGX1 | ||||||
Keywords | TRANSFERASE / NUCLEOTIDYLTRANSFERASE / ALTERNATIVE SPLICING | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Peneff, C. / Bourne, Y. | ||||||
Citation | Journal: EMBO J. / Year: 2001 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jv1.cif.gz | 224.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jv1.ent.gz | 177.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jv1_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1jv1_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1jv1_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 1jv1_validation.cif.gz | 69 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jv/1jv1 ftp://data.pdbj.org/pub/pdb/validation_reports/jv/1jv1 | HTTPS FTP |
-Related structure data
-Links
-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.) Homo sapiens (human) / Gene: UAP1 / Plasmid: pRU277 / Production host: Escherichia coli (E. coli) / Strain (production host): Xl1blue References: UniProt: Q16222, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.79 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2000 |
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: 1.89→39.84 Å / Num. all: 90578 / Num. obs: 90423 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 12.9 Å2 / Rsym value: 0.056 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 6349 / Rsym value: 0.305 / % possible all: 97.4 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 99.6 % / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS % possible obs: 97.4 % / Rmerge(I) obs: 0.305 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→37.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1907292 / 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: 47.7271 Å2 / ksol: 0.341741 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→37.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.22 / Rfactor Rwork: 0.183 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.251 / Rfactor Rwork: 0.208 |