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Open data
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Basic information
Entry | Database: PDB / ID: 8cc3 | |||||||||
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Title | Vibrio cholerae GbpA (LPMO domain) | |||||||||
![]() | GlcNAc-binding protein A | |||||||||
![]() | CELL ADHESION / Adhesin / LPMO / redox enzyme / colonization factor | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Montserrat-Canals, M. / Sorensen, H.V. / Cordara, G. / Krengel, U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. Authors: Sorensen, H.V. / Montserrat-Canals, M. / Loose, J.S.M. / Fisher, S.Z. / Moulin, M. / Blakeley, M.P. / Cordara, G. / Bjerregaard-Andersen, K. / Krengel, U. #1: ![]() Title: Human 2'-Deoxynucleoside 5'-Phosphate N -Hydrolase 1: Mechanism of 2'-Deoxyuridine 5'-Monophosphate Hydrolysis. Authors: Devi, S. / Carberry, A.E. / Zickuhr, G.M. / Dickson, A.L. / Harrison, D.J. / da Silva, R.G. #2: ![]() Title: Perdeuterated GbpA Enables Neutron Scattering Experiments of a Lytic Polysaccharide Monooxygenase. Authors: Sorensen, H.V. / Montserrat-Canals, M. / Loose, J.S.M. / Fisher, S.Z. / Moulin, M. / Blakeley, M.P. / Cordara, G. / Bjerregaard-Andersen, K. / Krengel, U. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 237.6 KB | Display | ![]() |
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PDB format | ![]() | 144.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 27.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8cc5C 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19820.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: gbpA, VCA0811 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 264 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 38.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2 M Zinc Acetate 0.1 M Sodium Cacodylate pH 6.5 18% w/v PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.128→47.14 Å / Num. obs: 221328 / % possible obs: 98.74 % / Redundancy: 2.2 % / CC1/2: 0.995 / Net I/σ(I): 6.13 |
Reflection shell | Resolution: 1.13→1.17 Å / Num. unique obs: 11391 / CC1/2: 0.219 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.128→47.135 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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