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- PDB-5nzg: Crystal structure of UDP-glucose pyrophosphorylase S374W mutant f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5nzg | ||||||
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Title | Crystal structure of UDP-glucose pyrophosphorylase S374W mutant from Leishmania major in complex with UDP-glucose | ||||||
![]() | UDP-glucose pyrophosphorylase | ||||||
![]() | TRANSFERASE / NTP-transferase / Pathogen / Allostery / Catalysis | ||||||
Function / homology | ![]() UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / nuclear lumen / ciliary plasm / glycogen metabolic process / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Hesse, R. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Decoding Allosteric Networks in Biocatalysts: Rational Approach to Therapies and Biotechnologies Authors: Cramer, J.T. / Fuehring, J.I. / Baruch, P. / Bruetting, C. / Knoelker, H.-J. / Gerardy-Schahn, R. / Fedorov, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.1 KB | Display | ![]() |
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PDB format | ![]() | 92.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 835.5 KB | Display | ![]() |
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Full document | ![]() | 841.9 KB | Display | |
Data in XML | ![]() | 24.8 KB | Display | |
Data in CIF | ![]() | 36.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5nzhC ![]() 5nziC ![]() 5nzjC ![]() 5nzkC ![]() 5nzlC ![]() 5nzmC ![]() 2m2aS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 56153.902 Da / Num. of mol.: 1 / Mutation: S374W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q4QDU3, UTP-glucose-1-phosphate uridylyltransferase | ||
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#2: Chemical | ChemComp-UPG / | ||
#3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.63 % / Mosaicity: 0.14 ° |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 24% PEG 3350, 100 mM Bis-Tris pH 6.8, 0.2 M Li2SO4, 2 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.82 Å / Num. obs: 78616 / % possible obs: 99.6 % / Redundancy: 13.11 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.022 / Net I/σ(I): 23.25 |
Reflection shell | Mean I/σ(I) obs: 2.88 / Num. unique all: 13410 / Rsym value: 0.354 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2M2A Resolution: 1.6→44.973 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→44.973 Å
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Refine LS restraints |
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LS refinement shell |
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