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Yorodumi- PDB-4mhy: Crystal structure of a glutaminyl cyclase from Ixodes scapularis ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mhy | ||||||
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Title | Crystal structure of a glutaminyl cyclase from Ixodes scapularis in complex with PBD150 | ||||||
Components | Glutaminyl cyclase, putativeGlutaminyl-peptide cyclotransferase | ||||||
Keywords | TRANSFERASE / alpha/beta-mixed fold / glutaminyl cyclase / PBD150 / secreted protein | ||||||
Function / homology | Function and homology information peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Ixodes scapularis (black-legged tick) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Huang, K.F. / Hsu, H.L. / Wang, A.H.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structural and functional analyses of a glutaminyl cyclase from Ixodes scapularis reveal metal-independent catalysis and inhibitor binding. Authors: Huang, K.F. / Hsu, H.L. / Karim, S. / 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 | 4mhy.cif.gz | 159.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mhy.ent.gz | 124.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mhy ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mhy | HTTPS FTP |
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-Related structure data
Related structure data | 4mhnC 4mhpC 4mhzC 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: 37808.660 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP RESIDUES 28-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ixodes scapularis (black-legged tick) / Gene: IscW_ISCW023264 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL References: UniProt: B7QK46, glutaminyl-peptide cyclotransferase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-PBD / |
#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: 2.07 Å3/Da / Density % sol: 40.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% (w/v) PEG 8000, 8% (v/v) ethylene glycol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Dec 5, 2012 |
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: 1.38→30 Å / Num. all: 64884 / Num. obs: 64300 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 31.3 |
Reflection shell | Resolution: 1.38→1.43 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AFM Resolution: 1.38→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.819 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 17.405 Å2
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Refinement step | Cycle: LAST / Resolution: 1.38→30 Å
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Refine LS restraints |
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