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Open data
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Basic information
Entry | Database: PDB / ID: 6bwc | ||||||
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Title | X-ray structure of Pen from Bacillus thuringiensis | ||||||
![]() | Polysaccharide biosynthesis protein CapD | ||||||
![]() | BIOSYNTHETIC PROTEIN / shout chain dehydrogenase / flagellin glycosylation / deoxy-sugar | ||||||
Function / homology | ![]() Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Delvaux, N.A. / Thoden, J.B. / Holden, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular architectures of Pen and Pal: Key enzymes required for CMP-pseudaminic acid biosynthesis in Bacillus thuringiensis. Authors: Delvaux, N.A. / Thoden, J.B. / Holden, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 396.8 KB | Display | ![]() |
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PDB format | ![]() | 325.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.2 MB | Display | ![]() |
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Full document | ![]() | 4.2 MB | Display | |
Data in XML | ![]() | 71.2 KB | Display | |
Data in CIF | ![]() | 94.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bwlC ![]() 2gn4S 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: 38774.598 Da / Num. of mol.: 6 / Mutation: D128N, K129A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: BTG_02000 / Production host: ![]() ![]() #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-UD1 / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2.2-2.5 M ammonium sulfate, 100 mM HEPES, 5 mM UDP-GlcNAc |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→86.66 Å / Num. obs: 55673 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5327 / Rsym value: 0.301 / % possible all: 84.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2gn4 Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.856 / SU B: 16.183 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.501 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→30 Å
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Refine LS restraints |
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