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Yorodumi- PDB-4fwu: Crystal structure of glutaminyl cyclase from drosophila melanogas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fwu | |||||||||
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Title | Crystal structure of glutaminyl cyclase from drosophila melanogaster in space group I4 | |||||||||
Components | CG32412 | |||||||||
Keywords | HYDROLASE / ALPHA/BETA HYDROLASE / PGLU FORMATION / ALZHEIMER`S DISEASE / PYROGLUTAMATE / PGLU-AMYLOID / GLYCOSYLATION | |||||||||
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 | Drosophila melanogaster (fruit fly) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Kolenko, P. / Koch, B. / Stubbs, M.T. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structure of glutaminyl cyclase from Drosophila melanogaster in space group I4. Authors: Kolenko, P. / Koch, B. / Rahfeld, J.U. / Schilling, S. / Demuth, H.U. / Stubbs, M.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fwu.cif.gz | 87.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fwu.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 4fwu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/4fwu ftp://data.pdbj.org/pub/pdb/validation_reports/fw/4fwu | HTTPS FTP |
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-Related structure data
Related structure data | 4f9uS 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 35341.672 Da / Num. of mol.: 1 / Fragment: unp residues 29-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: QC, CG10487, CG32412, Dmel_CG32412 / Plasmid: pPICZalphaB / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 References: UniProt: Q9VRQ9, glutaminyl-peptide cyclotransferase, Hydrolases; Acting on peptide bonds (peptidases) |
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#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 365 molecules
#3: Chemical | ChemComp-ZN / | ||||
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#4: Chemical | #5: Chemical | ChemComp-SO4 / #6: 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: 3.85 Å3/Da / Density % sol: 68.06 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.6M ammonium sulphate, 10% (v/v) 1,4-dioxane, 0.1M HEPES, 40mM MEGA-9, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Details: Varimax HR |
Radiation | Monochromator: Varimax HR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2→45 Å / Num. all: 35645 / Num. obs: 35641 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.5 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / Num. unique all: 4846 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4F9U Resolution: 2→45 Å / Cor.coef. Fo:Fc: 0.958 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.117 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.665 Å2
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Refinement step | Cycle: LAST / Resolution: 2→45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Num. reflection Rwork: 2376 / Total num. of bins used: 20 |