+Open data
-Basic information
Entry | Database: PDB / ID: 2afm | ||||||
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Title | Crystal structure of human glutaminyl cyclase at pH 6.5 | ||||||
Components | Glutaminyl-peptide cyclotransferase | ||||||
Keywords | TRANSFERASE / alpha-beta protein / metalloprotein | ||||||
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 / MAD / Resolution: 1.66 Å | ||||||
Authors | Huang, K.F. / Liu, Y.L. / Cheng, W.J. / Ko, T.P. / Wang, A.H.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Crystal structures of human glutaminyl cyclase, an enzyme responsible for protein N-terminal pyroglutamate formation Authors: Huang, K.F. / Liu, Y.L. / Cheng, W.J. / Ko, T.P. / Wang, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2afm.cif.gz | 153.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2afm.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 2afm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/2afm ftp://data.pdbj.org/pub/pdb/validation_reports/af/2afm | HTTPS FTP |
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-Related structure data
Related structure data | 2afoC 2afsC 2afuC 2afwC 2afxC 2afzC 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37557.398 Da / Num. of mol.: 2 / Fragment: residues 33-361 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) 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: 3.02 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: ammonium sulfate, dioxane, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 123 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9792, 0.9794, 0.9750 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2004 | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.66→50 Å / Num. all: 107174 / Num. obs: 106852 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 36.9 | ||||||||||||
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.66→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.66→50 Å
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Refine LS restraints |
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