[English] 日本語
Yorodumi- PDB-9fxh: Crystal structure of cobalt(II)-substituted double mutant Y115E Y... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9fxh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cobalt(II)-substituted double mutant Y115E Y117E human Glutaminyl Cyclase | ||||||
Components | Glutaminyl-peptide cyclotransferase | ||||||
Keywords | TRANSFERASE / human glutaminyl cyclase / acyltransferase / hQC / cobalt | ||||||
Function / homology | Function and homology information peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Tassone, G. / Pozzi, C. / Mangani, S. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: Int J Mol Sci / Year: 2024 Title: Metal Ion Binding to Human Glutaminyl Cyclase: A Structural Perspective. Authors: Tassone, G. / Pozzi, C. / Mangani, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 9fxh.cif.gz | 229.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb9fxh.ent.gz | 181.5 KB | Display | PDB format |
PDBx/mmJSON format | 9fxh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9fxh_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 9fxh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 9fxh_validation.xml.gz | 54.8 KB | Display | |
Data in CIF | 9fxh_validation.cif.gz | 77.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/9fxh ftp://data.pdbj.org/pub/pdb/validation_reports/fx/9fxh | HTTPS FTP |
-Related structure data
Related structure data | 9fxgC 9fxiC 9fxjC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
3 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 38894.789 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: PLASMID / Details (production host): pQE-80L / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q16769, glutaminyl-peptide cyclotransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.18 % |
---|---|
Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1-0.2 M ammonium sulphate and 0.1 M MES, pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.95374 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 3, 2023 |
Radiation | Monochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.76 Å / Num. obs: 50664 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 19.9 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.112 / Rrim(I) all: 0.194 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4761 / CC1/2: 0.747 / Rpim(I) all: 0.452 / Rrim(I) all: 0.772 / % possible all: 97 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→61.76 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.902 / SU B: 9.825 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.406 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.135 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.3→61.76 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|