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- PDB-3juk: The Crystal Structure of UDP-glucose pyrophosphorylase complexed ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3juk | ||||||
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Title | The Crystal Structure of UDP-glucose pyrophosphorylase complexed with UDP-glucose | ||||||
![]() | UDP-glucose pyrophosphorylase (GalU) | ||||||
![]() | TRANSFERASE / UDP-glucose pyrophosphorylase / Helicobacter pylori | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Kim, H. / Kim, K.K. | ||||||
![]() | ![]() Title: Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase Authors: Kim, H. / Choi, J. / Kim, T. / Lokanath, N.K. / Ha, S.C. / Suh, S.W. / Hwang, H.-Y. / Kim, K.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 238.3 KB | Display | ![]() |
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PDB format | ![]() | 191.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 54 KB | Display | |
Data in CIF | ![]() | 74.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jujSC 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
#1: Protein | Mass: 32086.932 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: O25363, UTP-glucose-1-phosphate uridylyltransferase #2: Chemical | ChemComp-UPG / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES-Na pH 7.5, 2% PEG 400, 1.5M ammonium sulfate, 10mM UDP-Glucose, 10 mM MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 54678 / Num. obs: 54022 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rsym value: 0.106 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.1 % / Num. unique all: 5102 / Rsym value: 0.368 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3JUJ Resolution: 2.3→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Bsol: 87.582 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 73 Å2 / Biso mean: 25.749 Å2 / Biso min: 4.72 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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Xplor file |
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