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- PDB-3pb9: Crystal structure of the catalytic domain of human Golgi-resident... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3pb9 | ||||||
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Title | Crystal structure of the catalytic domain of human Golgi-resident glutaminyl cyclase in complex with 1-benzylimidazole | ||||||
![]() | Glutaminyl-peptide cyclotransferase-like protein | ||||||
![]() | Transferase/Transferase inhibitor / alpha/beta protein / alpha/beta-mixed fold / glutaminyl cyclase / Golgi membrane / Transferase-Transferase inhibitor complex | ||||||
Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Golgi membrane / Golgi apparatus / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huang, K.F. / Liaw, S.S. / Huang, W.L. / Chia, C.Y. / Lo, Y.C. / Chen, Y.L. / Wang, A.H.J. | ||||||
![]() | ![]() Title: Structures of human Golgi-resident glutaminyl cyclase and its complexes with inhibitors reveal a large loop movement upon inhibitor binding Authors: Huang, K.F. / Liaw, S.S. / Huang, W.L. / Chia, C.Y. / Lo, Y.C. / Chen, Y.L. / Wang, A.H.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 | ![]() | 87.5 KB | Display | ![]() |
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PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 455.2 KB | Display | |
Data in XML | ![]() | 19.5 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3pb4SC ![]() 3pb6C ![]() 3pb7C ![]() 3pb8C ![]() 3pbbC ![]() 3pbeC 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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Unit cell |
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Components
#1: Protein | Mass: 37068.727 Da / Num. of mol.: 1 / Fragment: Golgi-luminal catalytic domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9NXS2, glutaminyl-peptide cyclotransferase |
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#2: Chemical | ChemComp-1BN / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 30%(v/v) PEG 200, 5%(w/v) PEG 3000, 0.1M Mes, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 2010 |
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: 1.12→30 Å / Num. all: 111121 / Num. obs: 107676 / % possible obs: 96.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 35.2 |
Reflection shell | Resolution: 1.12→1.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.2 / Num. unique all: 10975 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3PB4 Resolution: 1.12→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.974 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.413 Å2
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Refinement step | Cycle: LAST / Resolution: 1.12→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.12→1.149 Å / Total num. of bins used: 20
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