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Open data
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Basic information
Entry | Database: PDB / ID: 3h9g | ||||||
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Title | Crystal structure of E. coli MccB + MccA-N7isoASN | ||||||
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![]() | TRANSFERASE/ANTIBIOTIC / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ubiquitin-like modifier activating enzyme activity / defense response to bacterium / ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Regni, C.A. / Roush, R.F. / Miller, D. / Nourse, A. / Walsh, C.T. / Schulman, B.A. | ||||||
![]() | ![]() Title: How the MccB bacterial ancestor of ubiquitin E1 initiates biosynthesis of the microcin C7 antibiotic. Authors: Regni, C.A. / Roush, R.F. / Miller, D.J. / Nourse, A. / Walsh, C.T. / Schulman, B.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.6 KB | Display | ![]() |
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PDB format | ![]() | 229.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3h5aSC ![]() 3h5nC ![]() 3h5rC ![]() 3h9jC ![]() 3h9qC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 39409.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: thrombin cleavable His-tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | ![]() ![]() Details: MRTGNA-N7isoAsn was synthesized as previously described (Novoa et al, 1986; Roush et. al. 2008) Source: (synth.) ![]() ![]() ![]() #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.66 % |
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Crystal grow![]() | Temperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Tris-HCl pH 8.0, 50 mM (NH4)2SO4, 10 mM MccA-N7isoAsn, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2007 / Details: Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock high-resolution double crystal Si(220) sagital focusing Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→50 Å / Num. all: 60798 / Num. obs: 60798 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.065 / Χ2: 1.152 / Net I/σ(I): 21.914 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.371 / Num. unique all: 5645 / Χ2: 0.822 / % possible all: 90.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 3H5A Resolution: 2.2→46.88 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.249 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU B: 7.969 / SU ML: 0.202 / SU R Cruickshank DPI: 0.451 / SU Rfree: 0.263 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.451 / ESU R Free: 0.263 / 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 max: 78.59 Å2 / Biso mean: 36.297 Å2 / Biso min: 15.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→46.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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