+Open data
-Basic information
Entry | Database: PDB / ID: 8avq | ||||||
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Title | AO75L in Complex with UDP-Xylose | ||||||
Components | AO75L | ||||||
Keywords | TRANSFERASE / Glycosyltransferase / PBCV-1 / Xylosyltransferase / Glycans / VIRAL PROTEIN | ||||||
Function / homology | metal ion binding / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / Exostosin GT47 domain-containing protein Function and homology information | ||||||
Biological species | Paramecium bursaria Chlorella virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Laugeri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Poveda, A. / Lowary, T. / Van Etten, J.L. / Barbero, J.J. / De Castro, C. / Tonetti, M. / Rojas, A.L. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: AO75L in Complex with UDP-Xylose Authors: Laugeri, M.E. / Speciale, I. / Gimeno, A. / Lin, S. / Poveda, A. / Lowary, T. / Van Etten, J.L. / Barbero, J.J. / De Castro, C. / Tonetti, M. / Rojas, A.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8avq.cif.gz | 272.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8avq.ent.gz | 219 KB | Display | PDB format |
PDBx/mmJSON format | 8avq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8avq_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8avq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8avq_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 8avq_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/8avq ftp://data.pdbj.org/pub/pdb/validation_reports/av/8avq | HTTPS FTP |
-Related structure data
Related structure data | 8asaS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33788.672 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium bursaria Chlorella virus 1 / Gene: A075L / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q89410 |
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-Non-polymers , 7 types, 860 molecules
#2: Chemical | ChemComp-BCN / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-UDX / #5: Chemical | ChemComp-CA / #6: Chemical | ChemComp-MG / #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 0.1M TRIS; 0.1M BICINE, pH 8.1 37.5% Morpheus Precipitant mix4 0.03M CaCl2;0.03M MgCl2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 7, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→85.9 Å / Num. obs: 169521 / % possible obs: 99.4 % / Redundancy: 3.536 % / Biso Wilson estimate: 43.435 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.105 / Χ2: 0.87 / Net I/σ(I): 10.6 / Num. measured all: 599433 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8ASA Resolution: 2→85.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.719 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.83 Å2 / Biso mean: 38.184 Å2 / Biso min: 19.2 Å2
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Refinement step | Cycle: final / Resolution: 2→85.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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