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- PDB-2zel: Crystal structure of the human glutaminyl cyclase mutant D248A at... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zel | ||||||
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Title | Crystal structure of the human glutaminyl cyclase mutant D248A at 1.97 angstrom resolution | ||||||
![]() | Glutaminyl-peptide cyclotransferase | ||||||
![]() | TRANSFERASE / hydrogen bond network / glutaminyl cyclase / pyroglutamate / site-directed mutagenesis / proton transfer / Acyltransferase / Glycoprotein / Metal-binding | ||||||
Function / homology | ![]() 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 / zinc ion binding / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / Wang, A.H. | ||||||
![]() | ![]() Title: A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis. Authors: Huang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / 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 | ![]() | 157.1 KB | Display | ![]() |
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PDB format | ![]() | 122.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
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Full document | ![]() | 456.6 KB | Display | |
Data in XML | ![]() | 32.4 KB | Display | |
Data in CIF | ![]() | 49 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zedC ![]() 2zeeC ![]() 2zefC ![]() 2zegC ![]() 2zehC ![]() 2zemC ![]() 2zenC ![]() 2zeoC ![]() 2zepC ![]() 2afmS S: Starting model for refinement 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37513.387 Da / Num. of mol.: 2 / Fragment: residues 33-361 / Mutation: D248A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q16769, glutaminyl-peptide cyclotransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.32 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2%-4% dioxane, 1.6-1.8M ammonium sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 30, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→30 Å / Num. all: 64266 / Num. obs: 63945 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 30.1 |
Reflection shell | Resolution: 1.97→2.04 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6334 / Rsym value: 0.492 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2AFM Resolution: 1.97→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.4 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.97→2.04 Å / Rfactor Rfree error: 0.021
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