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Yorodumi- PDB-3r3i: Crystal Structure of C-terminal truncation of UDP-glucose Pyropho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r3i | ||||||
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Title | Crystal Structure of C-terminal truncation of UDP-glucose Pyrophosphorylase of Homo sapiens | ||||||
Components | UTP--glucose-1-phosphate uridylyltransferase | ||||||
Keywords | TRANSFERASE / Rossmann fold / beta barrel / nucleotidyltransferase | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis ...pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / D-glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis / brain development / extracellular exosome / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.57 Å | ||||||
Authors | Zheng, X. / Yu, Q. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of UDP-glucose Pyrophosphorylase of Homo sapiens Authors: Zheng, X. / Yu, Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r3i.cif.gz | 708.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r3i.ent.gz | 595.7 KB | Display | PDB format |
PDBx/mmJSON format | 3r3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/3r3i ftp://data.pdbj.org/pub/pdb/validation_reports/r3/3r3i | HTTPS FTP |
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-Related structure data
Related structure data | 3r2wS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 59184.402 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGP2, UGP1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase |
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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: 3.78 Å3/Da / Density % sol: 67.48 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: magnesium sulfate, PEG3350, glycerol, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 |
Detector | Type: MAR / Detector: CCD / Date: Oct 31, 2010 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.566→19.981 Å / Num. all: 43409 / Num. obs: 42839 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.095 |
Reflection shell | Resolution: 3.566→3.61 Å / Rmerge(I) obs: 0.649 / % possible all: 61.2 |
-Processing
Software |
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Refinement | Starting model: PDB ENTRY 3R2W Resolution: 3.57→19.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 91.284 / SU ML: 0.621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.603 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.14 Å2 / Biso mean: 175.894 Å2 / Biso min: 2.93 Å2
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Refinement step | Cycle: LAST / Resolution: 3.57→19.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.566→3.656 Å / Total num. of bins used: 20
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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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