+Open data
-Basic information
Entry | Database: PDB / ID: 6foa | ||||||
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Title | Human Xylosyltransferase 1 apo structure | ||||||
Components | Xylosyltransferase 1 | ||||||
Keywords | TRANSFERASE / Proteoglycan / Glycosyltransferase / Golgi / Xylosyltransferase | ||||||
Function / homology | Function and homology information protein xylosyltransferase / protein xylosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process ...protein xylosyltransferase / protein xylosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / proteoglycan biosynthetic process / glycosaminoglycan metabolic process / embryonic skeletal system development / ossification involved in bone maturation / Golgi membrane / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.869 Å | ||||||
Authors | Briggs, D.C. / Hohenester, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2018 Title: Structural Basis for the Initiation of Glycosaminoglycan Biosynthesis by Human Xylosyltransferase 1. Authors: 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 | 6foa.cif.gz | 413.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6foa.ent.gz | 339.6 KB | Display | PDB format |
PDBx/mmJSON format | 6foa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6foa_validation.pdf.gz | 453.3 KB | Display | wwPDB validaton report |
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Full document | 6foa_full_validation.pdf.gz | 453.8 KB | Display | |
Data in XML | 6foa_validation.xml.gz | 29 KB | Display | |
Data in CIF | 6foa_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/6foa ftp://data.pdbj.org/pub/pdb/validation_reports/fo/6foa | HTTPS FTP |
-Related structure data
Related structure data | 6ej7C 6ej8C 6ej9C 6ejaC 6ejbC 6ejcC 6ejdC 6ejeC 2gakS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 86122.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Plasmid: pCEP-Pu / Cell line (production host): HEK-293-F / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase |
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#2: Sugar | ChemComp-NAG / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 55-65% precipitant mix 2 (PEG8000 and ethylene glycol), 100 mM Bicine/Tris buffer at pH 7.5 100 mM of a sodium nitrate/sodium phosphate/ammonium sulphate mix. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 18, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.92819 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.869→86.81 Å / Num. obs: 74977 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Net I/σ(I): 9.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GAK Resolution: 1.869→76.629 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.84
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.19 Å2 / Biso mean: 37.4618 Å2 / Biso min: 13.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.869→76.629 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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