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Yorodumi- PDB-4fbe: Crystal structure of the C136A/C164A variant of mitochondrial iso... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fbe | ||||||
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Title | Crystal structure of the C136A/C164A variant of mitochondrial isoform of glutaminyl cyclase from Drosophila melanogaster | ||||||
Components | CG5976, isoform B | ||||||
Keywords | TRANSFERASE / HYDROLASE / alpha/beta hydrolase / pGlu formation / PE / Alzheimer's Disease / pyroglutamate / pGlu-amyloid | ||||||
Function / homology | Function and homology information peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / Neutrophil degranulation / mitochondrion / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Kolenko, P. / Koch, B. / Ruiz-Carilo, D. / Stubbs, M.T. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Crystal Structures of Glutaminyl Cyclases (QCs) from Drosophila melanogaster Reveal Active Site Conservation between Insect and Mammalian QCs. Authors: Koch, B. / Kolenko, P. / Buchholz, M. / Ruiz Carrillo, D. / Parthier, C. / Wermann, M. / Rahfeld, J.U. / Reuter, G. / Schilling, S. / Stubbs, M.T. / 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 | 4fbe.cif.gz | 145 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fbe.ent.gz | 111.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fbe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/4fbe ftp://data.pdbj.org/pub/pdb/validation_reports/fb/4fbe | HTTPS FTP |
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-Related structure data
Related structure data | 4f9uC 4f9vC 4faiSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37866.172 Da / Num. of mol.: 2 / Fragment: UNP residues 32-354 / Mutation: C136A, C164A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: isoQC, CG5976, Dmel_CG5976 / Plasmid: PQE31 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 References: UniProt: Q86PD7, glutaminyl-peptide cyclotransferase, Hydrolases; Acting on peptide bonds (peptidases) #2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: 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: 1.94 Å3/Da / Density % sol: 36.74 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG4000, 0.2 M magnesium chloride, 1 mM PQ50, 0.1 M Tris-HCl, pH 8.5, 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: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jul 10, 2010 / Details: MIRRORS |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→71.663 Å / Num. all: 36766 / Num. obs: 36763 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 1.9 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 1.88→1.99 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1926 / % possible all: 28.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FAI Resolution: 1.88→71.66 Å / Cor.coef. Fo:Fc: 0.945 / SU B: 2.261 / SU ML: 0.071 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: 14.238 Å2
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Refinement step | Cycle: LAST / Resolution: 1.88→71.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.88→1.933 Å / Total num. of bins used: 20
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