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Yorodumi- PDB-4f9v: Structure of C113A/C136A mutant variant of glycosylated glutaminy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f9v | |||||||||
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Title | Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from Drosophila melanogaster | |||||||||
Components | CG32412 | |||||||||
Keywords | TRANSFERASE / HYDROLASE / alpha/beta hydrolase / pGlu formation / PE / Alzheimer's Disease / pyroglutamate / pGlu-amyloid / glycosylation | |||||||||
Function / homology | Function and homology information 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 | 4f9v.cif.gz | 156.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f9v.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 4f9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/4f9v ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f9v | HTTPS FTP |
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-Related structure data
Related structure data | 4f9uSC 4faiC 4fbeC 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35277.543 Da / Num. of mol.: 2 / Fragment: UNP residues 29-340 / Mutation: C113A, C136A 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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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]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 |
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#3: 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, 690 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-PEG / | #7: 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: 3.42 Å3/Da / Density % sol: 64.02 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEG8000, 2 mM PQ50, 0.1 M MES, pH 6.5, 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: 2.1→147.973 Å / Num. all: 55222 / Num. obs: 55179 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.9 / Num. unique all: 8055 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4F9U Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 2.789 / SU ML: 0.074 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.155 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.132 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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