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Open data
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Basic information
Entry | Database: PDB / ID: 7xrf | |||||||||
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Title | Crystal structaure of DgpB/C complex | |||||||||
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![]() | LYASE / C-glycoside cleavage / isomerization | |||||||||
Function / homology | Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / metal ion binding / : / DUF6379 domain-containing protein / Xylose isomerase-like TIM barrel domain-containing protein![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ma, M. / He, P. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural mechanism of a dual-functional enzyme DgpA/B/C as both a C -glycoside cleaving enzyme and an O - to C -glycoside isomerase. Authors: He, P. / Wang, S. / Li, S. / Liu, S. / Zhou, S. / Wang, J. / Tao, J. / Wang, D. / Wang, R. / Ma, W. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 363.6 KB | Display | ![]() |
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PDB format | ![]() | 295.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 63.2 KB | Display | |
Data in CIF | ![]() | 88.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xr9C ![]() 7xreC ![]() 7exzS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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
#1: Protein | Mass: 36930.324 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dgpC / Production host: ![]() ![]() #2: Protein | Mass: 16062.067 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dgpB / Production host: ![]() ![]() #3: Chemical | ChemComp-MN / #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: 2.59 Å3/Da / Density % sol: 52.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M magnesium acetate and 10% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: May 6, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 226255 / % possible obs: 99.9 % / Redundancy: 14.5 % / CC1/2: 0.86 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.1→3.1 Å / Rmerge(I) obs: 0.86 / Num. unique obs: 689 / CC1/2: 0.85 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EXZ Resolution: 2.137→19.836 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.82 / Phase error: 31.61 / 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: 120.81 Å2 / Biso mean: 61.4346 Å2 / Biso min: 25.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.137→19.836 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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