+Open data
-Basic information
Entry | Database: PDB / ID: 7d17 | |||||||||||||||
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Title | Crystal structure of Macrostomum lignano glutaminyl cyclase | |||||||||||||||
Components | Glutaminyl-peptide cyclotransferase | |||||||||||||||
Keywords | TRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN | |||||||||||||||
Function / homology | glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Glutaminyl-peptide cyclotransferase Function and homology information | |||||||||||||||
Biological species | Macrostomum lignano (invertebrata) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.998 Å | |||||||||||||||
Authors | Huang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J. | |||||||||||||||
Funding support | Taiwan, 4items
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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 | 7d17.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d17.ent.gz | 59 KB | Display | PDB format |
PDBx/mmJSON format | 7d17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/7d17 ftp://data.pdbj.org/pub/pdb/validation_reports/d1/7d17 | HTTPS FTP |
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-Related structure data
Related structure data | 7d18C 7d1bC 7d1dC 7d1eC 7d1hC 7d1nC 7d1pC 7d1yC 7d21C 7d23C 7d2bC 7d2dC 7d2iC 7d2jC 4mhnS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 37405.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Macrostomum lignano (invertebrata) / Gene: BOX15_Mlig028993g1 / Production host: Escherichia coli (E. coli) References: UniProt: A0A267GXB9, glutaminyl-peptide cyclotransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.36 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M sodium HEPES, pH 7.5, 70% (v/v) 2-methyl-2,4-pentanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.98→30 Å / Num. obs: 6437 / % possible obs: 99.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 59.95 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.998→3.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 2 / Num. unique obs: 618 / % possible all: 99 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MHN Resolution: 2.998→29.466 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.73 / 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: 134.82 Å2 / Biso mean: 52.4904 Å2 / Biso min: 15.74 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.998→29.466 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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