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Yorodumi- PDB-7bvk: UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacill... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bvk | ||||||
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Title | UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P212121) | ||||||
Components | Oxidoreductase, NAD-binding | ||||||
Keywords | 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, NAD-binding Function and homology information | ||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Wangkanont, K. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bvk.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bvk.ent.gz | 100.2 KB | Display | PDB format |
PDBx/mmJSON format | 7bvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bvk_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7bvk_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7bvk_validation.xml.gz | 25.8 KB | Display | |
Data in CIF | 7bvk_validation.cif.gz | 34.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/7bvk ftp://data.pdbj.org/pub/pdb/validation_reports/bv/7bvk | HTTPS FTP |
-Related structure data
Related structure data | 7bvjSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35163.395 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: synthetic gene, codon optimized Source: (gene. exp.) Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455) (bacteria) Strain: ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455 / Gene: AFE_1457 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: B7JA34 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.94 % / Mosaicity: 0.28 ° |
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Crystal grow | Temperature: 289 K / Method: batch mode / pH: 5.5 Details: 100 mM Bis-Tris, 200 mM Ammonium Sulfate, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 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: 2.7→19.76 Å / Num. obs: 17552 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.086 / Rrim(I) all: 0.23 / Net I/σ(I): 6.5 / Num. measured all: 125291 / Scaling rejects: 86 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BVJ Resolution: 2.7→19.76 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 115.14 Å2 / Biso mean: 42.2284 Å2 / Biso min: 16.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→19.76 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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