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Yorodumi- PDB-3pbb: Crystal structure of human secretory glutaminyl cyclase in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pbb | ||||||
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Title | Crystal structure of human secretory glutaminyl cyclase in complex with PBD150 | ||||||
Components | Glutaminyl-peptide cyclotransferase | ||||||
Keywords | Transferase/Transferase inhibitor / alpha/beta protein / alpha/beta-mixed fold / glutaminyl cyclase / secretory pathway / Transferase-Transferase inhibitor complex | ||||||
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: 1.95 Å | ||||||
Authors | Huang, K.F. / Liaw, S.S. / Huang, W.L. / Chia, C.Y. / Lo, Y.C. / Chen, Y.L. / Wang, A.H.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pbb.cif.gz | 149.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pbb.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 3pbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/3pbb ftp://data.pdbj.org/pub/pdb/validation_reports/pb/3pbb | HTTPS FTP |
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-Related structure data
Related structure data | 3pb4C 3pb6C 3pb7C 3pb8C 3pb9C 3pbeC 2afmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37557.398 Da / Num. of mol.: 2 / Fragment: functional domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: pET 32a / Production host: Escherichia coli (E. coli) References: UniProt: Q16769, glutaminyl-peptide cyclotransferase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.7M (NH4)2SO4, 4%(v/v) dioxane, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 12, 2008 |
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: 1.95→50 Å / Num. all: 53608 / Num. obs: 53126 / % possible obs: 99.1 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.2 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5382 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2AFM Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 9.989 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.158 / 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: 40.412 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20
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