+Open data
-Basic information
Entry | Database: PDB / ID: 3h9q | ||||||
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Title | Crystal structure of E. coli MccB + SeMet MccA | ||||||
Components |
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Keywords | TRANSFERASE/ANTIBIOTIC / Ubiquitin-activating enzyme / microcin / bacteriocin / Mcc7 / peptide antibiotic / N-P bond formation / Antibiotic / Antimicrobial / Formylation / Phosphoprotein / TRANSFERASE / TRANSFERASE-ANTIBIOTIC COMPLEX | ||||||
Function / homology | Function and homology information URM1 activating enzyme activity / protein urmylation / tRNA wobble position uridine thiolation / sulfotransferase activity / thiosulfate sulfurtransferase activity / nucleotidyltransferase activity / defense response to bacterium / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.63 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 | 3h9q.cif.gz | 270.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3h9q.ent.gz | 216.7 KB | Display | PDB format |
PDBx/mmJSON format | 3h9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3h9q_validation.pdf.gz | 505.5 KB | Display | wwPDB validaton report |
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Full document | 3h9q_full_validation.pdf.gz | 547.6 KB | Display | |
Data in XML | 3h9q_validation.xml.gz | 53.3 KB | Display | |
Data in CIF | 3h9q_validation.cif.gz | 72.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/3h9q ftp://data.pdbj.org/pub/pdb/validation_reports/h9/3h9q | HTTPS FTP |
-Related structure data
Related structure data | 3h5aC 3h5nC 3h5rC 3h9gC 3h9jSC 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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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.) Escherichia coli (E. coli) / Strain: BM7006 / Gene: mccB / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q47506 #2: Protein/peptide | Type: Polypeptide / Class: Inhibitor / Mass: 810.739 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: MccA peptide was synthesized and reverse-phase HPLC purified by the Hartwell Center for Bioinformatics and Biotechnology at St. Jude Children's Research Hospital Source: (synth.) Escherichia coli (E. coli) References: UniProt: Q47505, Selenomethionine derivative of Microcin C7 #3: Chemical | ChemComp-ZN / #4: Chemical | #5: 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: 1.97 Å3/Da / Density % sol: 37.63 % |
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Crystal grow | Temperature: 291.2 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24-26% Pentaerythritol ethoxylate (15/4 EO/OH, Hampton Research), 50 mM Bis-Tris pH 6.5, 50 mM (NH4)2SO4, 10 mM SeMet-MccA, 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: 24-ID-E / Wavelength: 0.97926 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2007 Details: Vertical and horizontal focusing mirrors in Kirkpatrick-Baez geometry. |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(111) side bounce, optional Si(311) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→20 Å / Num. all: 37055 / Num. obs: 37055 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.082 / Net I/σ(I): 23.312 |
Reflection shell | Resolution: 2.63→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.311 / Num. unique all: 3683 / Χ2: 0.546 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3H9J Resolution: 2.63→20 Å / Occupancy max: 1 / Occupancy min: 0 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Bsol: 27.884 Å2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.34 Å2 / Biso mean: 51.983 Å2 / Biso min: 19.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.63→20 Å
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Refine LS restraints |
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Xplor file |
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