+Open data
-Basic information
Entry | Database: PDB / ID: 6eja | ||||||
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Title | Human Xylosyltransferase 1 in complex with peptide QEEEYSGGGQGG | ||||||
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 / chondroitin sulfate biosynthetic process / Golgi cis cisterna / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan 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 / 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 / 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 / nuclear membrane / collagen-containing extracellular matrix / mitochondrial inner membrane / oxidoreductase activity / blood microparticle / 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 / Resolution: 1.94 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 | 6eja.cif.gz | 411.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eja.ent.gz | 339.7 KB | Display | PDB format |
PDBx/mmJSON format | 6eja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eja_validation.pdf.gz | 437.6 KB | Display | wwPDB validaton report |
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Full document | 6eja_full_validation.pdf.gz | 441.4 KB | Display | |
Data in XML | 6eja_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 6eja_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/6eja ftp://data.pdbj.org/pub/pdb/validation_reports/ej/6eja | HTTPS FTP |
-Related structure data
Related structure data | 6ej7C 6ej8C 6ej9C 6ejbC 6ejcC 6ejdC 6ejeC 6foaC 2gamS 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 / Fragment: UNP residues 232-959 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: XYLT1, XT1 / Plasmid: pCEP-Pu / Cell line (production host): HEK293FS / Production host: Homo sapiens (human) / References: UniProt: Q86Y38, protein xylosyltransferase |
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#2: Protein/peptide | Mass: 1197.125 Da / Num. of mol.: 1 / Fragment: UNP residues 210-221 / Mutation: G214Y, L220G, V221G / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02760 |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.48 Å3/Da / Density % sol: 50.35 % |
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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 0.1M of NPS mix (0.033M of each) |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 23, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.94→43.48 Å / Num. obs: 64274 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 39.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.041 / Rrim(I) all: 0.087 / Net I/σ(I): 8.7 / Num. measured all: 267755 / Scaling rejects: 0 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2GAM Resolution: 1.94→40.184 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.04
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.32 Å2 / Biso mean: 56.5414 Å2 / Biso min: 27.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.94→40.184 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: 23
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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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