+Open data
-Basic information
Entry | Database: PDB / ID: 3h5n | ||||||
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Title | Crystal structure of E. coli MccB + ATP | ||||||
Components | MccB protein | ||||||
Keywords | TRANSFERASE / Ubiquitin-activating enzyme / microcin / protein structure / MccC7 / peptide antibiotics / N-P bond formation | ||||||
Function / homology | Function and homology information ubiquitin-like modifier activating enzyme activity / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Regni, C.A. / Roush, R.F. / Miller, D. / Nourse, A. / Walsh, C.T. / Schulman, B.A. | ||||||
Citation | Journal: Embo J. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3h5n.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h5n.ent.gz | 228.4 KB | Display | PDB format |
PDBx/mmJSON format | 3h5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/3h5n ftp://data.pdbj.org/pub/pdb/validation_reports/h5/3h5n | HTTPS FTP |
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-Related structure data
Related structure data | 3h5aSC 3h5rC 3h9gC 3h9jC 3h9qC 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#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.) Escherichia coli (E. coli) / Strain: BM7006 / Gene: mccB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47506 |
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-Non-polymers , 5 types, 744 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / #5: Chemical | ChemComp-SO4 / | #6: 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: 1.96 Å3/Da / Density % sol: 37.32 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Na Hepes pH 7.5, 100 mM MgSO4, 25 mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 291.2K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97926 Å |
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: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. all: 96263 / Num. obs: 96263 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.026 / Net I/σ(I): 19.166 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.364 / Num. unique all: 9202 / Χ2: 1.036 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3H5A Resolution: 1.9→42.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.254 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.787 / SU B: 4.708 / SU ML: 0.136 / SU R Cruickshank DPI: 0.217 / SU Rfree: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.186 / 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: 75.74 Å2 / Biso mean: 22.839 Å2 / Biso min: 8.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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