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- PDB-4d48: Crystal Structure of glucose-1-phosphate uridylyltransferase GalU... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4d48 | ||||||
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Title | Crystal Structure of glucose-1-phosphate uridylyltransferase GalU from Erwinia amylovora. | ||||||
![]() | GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE | ||||||
![]() | TRANSFERASE / AMYLOVORAN BIOSYNTHESIS / UDP-GLUCOSE / FIRE BLIGHT | ||||||
Function / homology | ![]() UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toccafondi, M. / Wuerges, J. / Cianci, M. / Benini, S. | ||||||
![]() | ![]() Title: Glucose-1-phosphate uridylyltransferase from Erwinia amylovora: Activity, structure and substrate specificity. Authors: Benini, S. / Toccafondi, M. / Rejzek, M. / Musiani, F. / Wagstaff, B.A. / Wuerges, J. / Cianci, M. / Field, R.A. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014 Title: Expression, purification, crystallization and preliminary X-ray analysis of glucose-1-phosphate uridylyltransferase (GalU) from Erwinia amylovora. Authors: Toccafondi, M. / Cianci, M. / Benini, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.3 KB | Display | ![]() |
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PDB format | ![]() | 187 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.2 KB | Display | ![]() |
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Full document | ![]() | 419.5 KB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 19.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2e3dS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.466, 0.8848, -0.001262), Vector: |
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Components
#1: Protein | Mass: 32922.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: D4I3X5, UTP-glucose-1-phosphate uridylyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.09 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 2M AMMONIUM SULFATE, 0.1 M TRIS PH 8.5, 5% ETHYLENE GLYCOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2014 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→66.66 Å / Num. obs: 12434 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 57.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.46→2.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2E3D Resolution: 2.46→64.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.167 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.658 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE FOLLOWING RESIDUES WERE DISORDERED 1-4, 84-87, 233-238, 299-302
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.542 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→64.66 Å
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Refine LS restraints |
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