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- PDB-7d18: Crystal structure of Acidobacteriales bacterium glutaminyl cyclase -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d18 | ||||||
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Title | Crystal structure of Acidobacteriales bacterium glutaminyl cyclase | ||||||
![]() | Peptidase M28 | ||||||
![]() | TRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN | ||||||
Function / homology | Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / acyltransferase activity / Peptidase M28![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Unique Carboxylic-Acid Hydrogen-Bond Network (CAHBN) Confers Glutaminyl Cyclase Activity on M28 Family Enzymes. Authors: Huang, K.F. / Huang, J.S. / Wu, M.L. / Hsieh, W.L. / Hsu, K.C. / Hsu, H.L. / Ko, T.P. / Wang, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146.9 KB | Display | ![]() |
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PDB format | ![]() | 113.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 455.2 KB | Display | |
Data in XML | ![]() | 16.6 KB | Display | |
Data in CIF | ![]() | 25.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d17C ![]() 7d1bC ![]() 7d1dC ![]() 7d1eC ![]() 7d1hC ![]() 7d1nC ![]() 7d1pC ![]() 7d1yC ![]() 7d21C ![]() 7d23C ![]() 7d2bC ![]() 7d2dC ![]() 7d2iC ![]() 7d2jC 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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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32564.648 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BGO25_06485 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 346 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-NA / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | ChemComp-TRS / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 31.15 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M (NH4)2SO4, 0.1 M sodium cacodylate, pH 6.5, 30% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→30 Å / Num. obs: 53659 / % possible obs: 98.5 % / Redundancy: 10 % / Biso Wilson estimate: 13.73 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.33→1.38 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 5037 / % possible all: 92.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 63.04 Å2 / Biso mean: 18.5238 Å2 / Biso min: 9.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.332→25.909 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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