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Yorodumi- PDB-7d18: Crystal structure of Acidobacteriales bacterium glutaminyl cyclase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d18 | ||||||
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Title | Crystal structure of Acidobacteriales bacterium glutaminyl cyclase | ||||||
Components | Peptidase M28 | ||||||
Keywords | TRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN | ||||||
Function / homology | Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / acyltransferase activity / Peptidase M28 Function and homology information | ||||||
Biological species | Acidobacteriales bacterium 59-55 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.332 Å | ||||||
Authors | Huang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: J.Mol.Biol. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d18.cif.gz | 146.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d18.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 7d18.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/7d18 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/7d18 | HTTPS FTP |
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-Related structure data
Related structure data | 7d17C 7d1bC 7d1dC 7d1eC 7d1hC 7d1nC 7d1pC 7d1yC 7d21C 7d23C 7d2bC 7d2dC 7d2iC 7d2jC C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Acidobacteriales bacterium 59-55 (bacteria) Gene: BGO25_06485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q3QTC5 |
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-Non-polymers , 6 types, 346 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å |
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: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.332→25.909 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 11.86 / 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: 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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