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- PDB-3pid: The apo-form UDP-glucose 6-dehydrogenase with a C-terminal six-hi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pid | ||||||
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Title | The apo-form UDP-glucose 6-dehydrogenase with a C-terminal six-histidine tag | ||||||
![]() | UDP-glucose 6-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Rossmann Fold / Dehydrogenase | ||||||
Function / homology | ![]() UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / polysaccharide biosynthetic process / NAD binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chen, Y.-Y. / Ko, T.-P. / Lin, C.-H. / Chen, W.-H. / Wang, A.H.-J. | ||||||
![]() | ![]() Title: Conformational change upon product binding to Klebsiella pneumoniae UDP-glucose dehydrogenase: a possible inhibition mechanism for the key enzyme in polymyxin resistance. Authors: Chen, Y.Y. / Ko, T.P. / Lin, C.H. / Chen, W.H. / Wang, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.5 KB | Display | ![]() |
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PDB format | ![]() | 81.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.2 KB | Display | ![]() |
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Full document | ![]() | 438.3 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 38.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3phlC ![]() 3pjgC ![]() 3plnC ![]() 3plrC ![]() 1dliS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 48456.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: C4XAX5, UniProt: A0A0J9WZA6*PLUS, UDP-glucose 6-dehydrogenase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.1M Tris-HCl buffer (pH 8.0), 0.8M sodium formate (Fluka), 14 % (w/v) PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2006 / Details: mirrors |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 96000 / Num. obs: 94272 / % possible obs: 98.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.35 / Net I/σ(I): 49.7 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3 / Num. unique all: 8420 / % possible all: 86.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DLI Resolution: 1.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.45 Å / Rfactor Rfree error: 0.0269
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