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- PDB-7d8e: Crystal Structure of double mutant Y115E Y117E human Secretory Gl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d8e | ||||||
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Title | Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09 | ||||||
![]() | Glutaminyl-peptide cyclotransferase | ||||||
![]() | TRANSFERASE / Glutaminyl-peptide cyclotransferase / sQC / Alzheimer's disease / Pyroglutamate | ||||||
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 / extracellular exosome / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of double mutant Y115E Y117E human Secretory Glutaminyl Cyclase in complex with LSB-09 Authors: Dileep, K.V. / Ihara, K. / Sakai, N. / Shirozu, M. / Zhang, K.Y.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 389.2 KB | Display | ![]() |
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PDB format | ![]() | 316.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4ywyS S: Starting model for refinement |
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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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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
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 37489.277 Da / Num. of mol.: 3 / Mutation: Y115E, Y117E Source method: isolated from a genetically manipulated source Details: Cpd-09 / Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q16769, glutaminyl-peptide cyclotransferase |
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-Non-polymers , 5 types, 364 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GYO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GYO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.34 % / Description: Hexagonal plate like crystals |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 100 mM MES buffer pH 6.0-6.5, 46-67 mM NaOH, 100 mM ammonium sulfate PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 22, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→46.85 Å / Num. obs: 79687 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Net I/σ(I): 12.9 / Num. measured all: 611144 / Scaling rejects: 32 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4YWY Resolution: 2→46.85 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.05 / 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: 72.86 Å2 / Biso mean: 18.19 Å2 / Biso min: 4.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.85 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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