+Open data
-Basic information
Entry | Database: PDB / ID: 3si1 | |||||||||
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Title | Structure of glycosylated murine glutaminyl cyclase | |||||||||
Components | Glutaminyl-peptide cyclotransferase | |||||||||
Keywords | TRANSFERASE / alpha/beta hydrolase / Alzheimer's disease / pyroglutamate / pGlu / pE / pGlu-amyloid / glycosylation / glycoprotein | |||||||||
Function / homology | Function and homology information peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Neutrophil degranulation / zinc ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å | |||||||||
Authors | Dambe, T. / Carrillo, D. / Parthier, C. / Stubbs, M.T. | |||||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structures of Glycosylated Mammalian Glutaminyl Cyclases Reveal Conformational Variability near the Active Center. Authors: Ruiz-Carrillo, D. / Koch, B. / Parthier, C. / Wermann, M. / Dambe, T. / Buchholz, M. / Ludwig, H.H. / Heiser, U. / Rahfeld, J.U. / Stubbs, M.T. / Schilling, S. / Demuth, H.U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3si1.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3si1.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 3si1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/si/3si1 ftp://data.pdbj.org/pub/pdb/validation_reports/si/3si1 | HTTPS FTP |
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-Related structure data
Related structure data | 3si0C 3si2C 2afmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37606.543 Da / Num. of mol.: 1 / Fragment: UNP residues 36-362 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Qpct / Plasmid: pPICZalphaB / Production host: Pichia pastoris (fungus) / Strain (production host): X33 References: UniProt: Q9CYK2, glutaminyl-peptide cyclotransferase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 100 mM sodium acetate, 200 mM ammonium sulfate, 12% w/v PEG2000 MME, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 2, 2007 |
Radiation | Monochromator: BL14.1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→19.753 Å / Num. all: 8528 / Num. obs: 8528 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 56.2 Å2 / Rsym value: 0.111 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.508 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AFM Resolution: 2.9→19.753 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.85 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.393 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.514 / 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 max: 87.85 Å2 / Biso mean: 48.3409 Å2 / Biso min: 8.62 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→19.753 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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