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- PDB-8rr2: 3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8rr2 | ||||||
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Title | 3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto-glucose | ||||||
![]() | 3-keto-disaccharide hydrolase domain-containing protein | ||||||
![]() | LYASE / Product Complex | ||||||
Function / homology | 3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / : / Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pfeiffer, M. / Kastner, K. / Oberdorfer, G. / Nidetzky, B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway. Authors: Kastner, K. / Bitter, J. / Pfeiffer, M. / Grininger, C. / Oberdorfer, G. / Pavkov-Keller, T. / Weber, H. / Nidetzky, B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 39.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ro4C 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30987.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BSIG_4447, Btheta7330_00884 Production host: ![]() ![]() References: UniProt: A0A0P0FHP3 |
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-Non-polymers , 5 types, 571 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5 35% pentaerythritol ethoxylate, 6% polyvinlypirolidone Soaking for 90 minutes with 20 mM 3-keto-sucrose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 30, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→48.71 Å / Num. obs: 65902 / % possible obs: 99.83 % / Redundancy: 13.5 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2064 / Rpim(I) all: 0.0767 / Rrim(I) all: 0.2847 / Net I/av σ(I): 8.03 / Net I/σ(I): 8.03 |
Reflection shell | Resolution: 1.78→1.844 Å / Mean I/σ(I) obs: 0.62 / Num. unique obs: 83345 / CC1/2: 0.416 / CC star: 0.766 / % possible all: 99.75 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: AlphaFold2 Resolution: 1.74→48.71 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3312 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 29.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→48.71 Å
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Refine LS restraints |
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LS refinement shell |
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