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- PDB-7d1p: Crystal structure of Ixodes scapularis glutaminyl cyclase with th... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d1p | ||||||
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Title | Crystal structure of Ixodes scapularis glutaminyl cyclase with three Cd ions bound to the active site | ||||||
![]() | Glutaminyl-peptide cyclotransferase | ||||||
![]() | TRANSFERASE / Glutaminyl cyclase / METAL BINDING PROTEIN | ||||||
Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Huang, K.-F. / Huang, J.-S. / Wu, M.-L. / Hsieh, W.-L. / Wang, A.H.-J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.8 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.2 KB | Display | ![]() |
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Full document | ![]() | 447.3 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 20.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7d17C ![]() 7d18C ![]() 7d1bC ![]() 7d1dC ![]() 7d1eC ![]() 7d1hC ![]() 7d1nC ![]() 7d1yC ![]() 7d21C ![]() 7d23C ![]() 7d2bC ![]() 7d2dC ![]() 7d2iC ![]() 7d2jC ![]() 4mhnS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 38248.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B7QK46, glutaminyl-peptide cyclotransferase | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-BCT / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10%(w/v) PEG8000, 8%(v/v) ethylene glycol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Oct 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.36→30 Å / Num. obs: 13295 / % possible obs: 98.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.36→2.44 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1183 / % possible all: 90.6 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MHN Resolution: 2.36→25.27 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.88 / SU B: 9.156 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.713 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 123.78 Å2 / Biso mean: 34.356 Å2 / Biso min: 6.45 Å2
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Refinement step | Cycle: final / Resolution: 2.36→25.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.362→2.423 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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