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Yorodumi- PDB-6ej7: Human Xylosyltransferase 1 in complex with UDP-xylose and peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ej7 | ||||||
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Title | Human Xylosyltransferase 1 in complex with UDP-xylose and peptide QEEEGAGGGQGG | ||||||
Components |
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Keywords | TRANSFERASE / Proteoglycan / Glycosyltransferase / Golgi / Xylosyltransferase | ||||||
Function / homology | Function and homology information protein xylosyltransferase / protein xylosyltransferase activity / Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic process / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process ...protein xylosyltransferase / protein xylosyltransferase activity / Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / chondroitin sulfate proteoglycan biosynthetic process / glycosaminoglycan metabolic 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 / IgA binding / embryonic skeletal system development / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / ossification involved in bone maturation / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / collagen-containing extracellular matrix / blood microparticle / nuclear membrane / mitochondrial inner membrane / oxidoreductase activity / cell adhesion / Golgi membrane / heme binding / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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 | 6ej7.cif.gz | 435.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ej7.ent.gz | 357.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ej7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6ej7 ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6ej7 | HTTPS FTP |
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-Related structure data
Related structure data | 6ej8C 6ej9C 6ejaC 6ejbC 6ejcC 6ejdC 6ejeC 6foaC 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
-Protein / Protein/peptide / Sugars , 3 types, 3 molecules AB
#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): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase |
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#2: Protein/peptide | Mass: 1075.003 Da / Num. of mol.: 1 / Mutation: S215A, L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760 |
#3: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 383 molecules
#4: Chemical | ChemComp-UDX / | ||||||
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#5: Chemical | ChemComp-NA / | ||||||
#6: Chemical | ChemComp-PO4 / #7: Chemical | ChemComp-EDO / #8: Chemical | #9: 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: 2.72 Å3/Da / Density % sol: 54.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 55-65% Morpheus precipitant mix 2 (PEG8000 and ethylene glycol), 0.1M Bicine/Tris buffer at pH 7.5 0.1 M of Morpheus NPS mix. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 21, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→86.89 Å / Num. obs: 61497 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 30.33 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.077 / Rrim(I) all: 0.198 / Net I/σ(I): 9 / Num. measured all: 400825 / Scaling rejects: 0 | ||||||||||||||||||||||||
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: 2→76.455 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.04 Å2 / Biso mean: 45.9448 Å2 / Biso min: 19.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→76.455 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22 / % reflection obs: 100 %
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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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