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Yorodumi- PDB-1kws: CRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX W... -
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-Basic information
Entry | Database: PDB / ID: 1kws | ||||||
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Title | CRYSTAL STRUCTURE OF BETA1,3-GLUCURONYLTRANSFERASE I IN COMPLEX WITH THE ACTIVE UDP-GLCUA DONOR | ||||||
Components | BETA-1,3-GLUCURONYLTRANSFERASE 3 | ||||||
Keywords | TRANSFERASE / DXD / NTP binding domain | ||||||
Function / homology | Function and homology information dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / positive regulation of intracellular protein transport ...dermatan sulfate proteoglycan biosynthetic process / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase / galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity / chondroitin sulfate proteoglycan biosynthetic process / glucuronosyltransferase activity / Defective B3GAT3 causes JDSSDHD / A tetrasaccharide linker sequence is required for GAG synthesis / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / positive regulation of intracellular protein transport / cis-Golgi network / positive regulation of catalytic activity / protein glycosylation / protein phosphatase activator activity / carbohydrate metabolic process / Golgi membrane / Golgi apparatus / extracellular exosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å | ||||||
Authors | Pedersen, L.C. / Darden, T.A. / Negishi, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA. Authors: Pedersen, L.C. / Darden, T.A. / Negishi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kws.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kws.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kws.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kws_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1kws_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1kws_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 1kws_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/1kws ftp://data.pdbj.org/pub/pdb/validation_reports/kw/1kws | HTTPS FTP |
-Related structure data
Related structure data | 1fggS S: Starting model for refinement |
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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: 28992.064 Da / Num. of mol.: 2 / Fragment: Residue 76-335 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O94766 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.43 Å3/Da / Density % sol: 49.38 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6 Details: MES, MME-PEG2K, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 296K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 9, 2000 / Details: Yale Mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→25 Å / Num. all: 32779 / Num. obs: 32764 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.67 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3 / Num. unique all: 3134 / % possible all: 96 |
Reflection | *PLUS Num. obs: 32779 / Num. measured all: 112504 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS % possible obs: 96 % / Rmerge(I) obs: 0.309 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1FGG Resolution: 2.1→24.68 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 139032.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.4552 Å2 / ksol: 0.351798 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→24.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.188 / Rfactor obs: 0.187 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.187 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.262 / Rfactor Rwork: 0.22 / Rfactor obs: 0.22 |