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Yorodumi- PDB-2zeo: Crystal structure of the human glutaminyl cyclase mutant D305E at... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zeo | ||||||
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Title | Crystal structure of the human glutaminyl cyclase mutant D305E at 1.66 angstrom resolution | ||||||
Components | Glutaminyl-peptide cyclotransferase | ||||||
Keywords | TRANSFERASE / hydrogen bond network / glutaminyl cyclase / pyroglutamate / site-directed mutagenesis / proton transfer / Acyltransferase / Glycoprotein / Metal-binding | ||||||
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 / FOURIER SYNTHESIS / Resolution: 1.66 Å | ||||||
Authors | Huang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / Wang, A.H. | ||||||
Citation | Journal: Biochem.J. / Year: 2008 Title: A conserved hydrogen-bond network in the catalytic centre of animal glutaminyl cyclases is critical for catalysis. Authors: Huang, K.F. / Wang, Y.R. / Chang, E.C. / Chou, T.L. / 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 | 2zeo.cif.gz | 159.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zeo.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 2zeo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/2zeo ftp://data.pdbj.org/pub/pdb/validation_reports/ze/2zeo | HTTPS FTP |
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-Related structure data
Related structure data | 2zedC 2zeeC 2zefC 2zegC 2zehC 2zelC 2zemC 2zenC 2zepC 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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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 37571.426 Da / Num. of mol.: 2 / Fragment: residues 33-361 / Mutation: D305E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: bone marrow / Gene: QPCT / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: 3.03 Å3/Da / Density % sol: 59.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2%-4% dioxane, 1.6-1.8M ammonium sulfate, 100mM Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 315 / Detector: CCD / Date: Aug 30, 2006 / Details: mirrors |
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: 1.66→30 Å / Num. all: 107287 / Num. obs: 106858 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 33.6 |
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.6 / Num. unique all: 10658 / Rsym value: 0.495 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2AFM Resolution: 1.66→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.5 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.72 Å / Rfactor Rfree error: 0.01
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