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- PDB-4mhz: Crystal structure of apo-form glutaminyl cyclase from Ixodes scap... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mhz | ||||||
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Title | Crystal structure of apo-form glutaminyl cyclase from Ixodes scapularis in complex with PBD150 | ||||||
![]() | Glutaminyl cyclase, putative![]() | ||||||
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Function / homology | ![]() peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Huang, K.F. / Hsu, H.L. / Wang, A.H.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.3 KB | Display | ![]() |
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PDB format | ![]() | 63.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4mhnC ![]() 4mhpC ![]() 4mhyC ![]() 2afmS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() ![]() References: UniProt: B7QK46, ![]() |
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#2: Chemical | ChemComp-PBD / |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.27 % |
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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, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 4, 2012 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.95→50 Å / Num. all: 23824 / Num. obs: 21418 / % possible obs: 89.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 1.7 / Num. unique all: 2102 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2AFM Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.795 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.214 / 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: 21.424 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.952→2.003 Å / Total num. of bins used: 20
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