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- PDB-7bvj: UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacill... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bvj | ||||||
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Title | UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21) | ||||||
![]() | Oxidoreductase, NAD-binding | ||||||
![]() | OXIDOREDUCTASE / GnnA / UDP-GlcNAc / lipopolysaccharide / UDP-N-acetylglucosamine 3-dehydrogenase | ||||||
Function / homology | Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / Chem-F8U / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, NAD-binding![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wangkanont, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biochemical and Structural Investigation of GnnA in the Lipopolysaccharide Biosynthesis Pathway of Acidithiobacillus ferrooxidans . Authors: Manissorn, J. / Sitthiyotha, T. / Montalban, J.R.E. / Chunsrivirot, S. / Thongnuek, P. / Wangkanont, 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 | ![]() | 263.1 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7bvkC ![]() 3ezyS ![]() 4fb5S ![]() 4h3vS ![]() 4hktS ![]() 4koaS ![]() 5yabS 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: 35163.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455 / Gene: AFE_1457 / Plasmid: pET24a / Production host: ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-F8U / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.42 % / Mosaicity: 0.29 ° |
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Crystal grow | Temperature: 289 K / Method: batch mode / pH: 5.5 / Details: 100 mM Bis-Tris, 200 mM NaCl, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2019 | |||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999999 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.15→19.8 Å / Num. obs: 66811 / % possible obs: 99.8 % / Redundancy: 7.5 % / CC1/2: 0.976 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.115 / Rrim(I) all: 0.315 / Net I/σ(I): 5.1 / Num. measured all: 499713 / Scaling rejects: 1804 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.7 %
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4koa, 4h3v, 4fb5, 5yab, 4hkt, 3ezy Resolution: 2.15→19.8 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.15 Å2 / Biso mean: 30.5095 Å2 / Biso min: 9.85 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.15→19.8 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %
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