+Open data
-Basic information
Entry | Database: PDB / ID: 8og4 | |||||||||
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Title | Exostosin-like 3 UDP complex | |||||||||
Components | Exostosin-like 3 | |||||||||
Keywords | TRANSFERASE / Glycosyltransferase / heparan sulfate | |||||||||
Function / homology | : / URIDINE-5'-DIPHOSPHATE / : Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Sammon, D. / Hohenester, E. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2023 Title: Molecular mechanism of decision-making in glycosaminoglycan biosynthesis. Authors: Sammon, D. / Krueger, A. / Busse-Wicher, M. / Morgan, R.M. / Haslam, S.M. / Schumann, B. / Briggs, D.C. / Hohenester, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8og4.cif.gz | 685 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8og4.ent.gz | 456.3 KB | Display | PDB format |
PDBx/mmJSON format | 8og4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8og4_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 8og4_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 8og4_validation.xml.gz | 50.2 KB | Display | |
Data in CIF | 8og4_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/8og4 ftp://data.pdbj.org/pub/pdb/validation_reports/og/8og4 | HTTPS FTP |
-Related structure data
Related structure data | 8og1C 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 101613.000 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXTL3, EXTL1L, EXTR1, KIAA0519 / Production host: Homo sapiens (human) References: UniProt: O43909, glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 3 types, 78 molecules
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.73 Å3/Da / Density % sol: 54.89 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 12.5% (w/v) PEG3350, 0.1 M malic acid, pH 7.0. Soaked overnight in 15% PEG 3350, 0.1 M malic acid, pH 7.0, 5 mM UDP and 5 mM MnCl2. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9212 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→55.16 Å / Num. obs: 129790 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 54.46 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.048 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.1→2.14 Å / Num. unique obs: 6395 / CC1/2: 0.255 / Rpim(I) all: 0.986 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20.52 Å / SU ML: 0.3258 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7477 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 65.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→20.52 Å
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Refine LS restraints |
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LS refinement shell |
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