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Yorodumi- PDB-3r9f: Crystal structure of Microcin C7 self immunity acetyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3r9f | ||||||
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Title | Crystal structure of Microcin C7 self immunity acetyltransferase MccE in complex with Coenzyme A and Glutamyl sulfamoyl adenosine (ESA) | ||||||
Components | MccE protein | ||||||
Keywords | TRANSFERASE / Microcin C7 / Acetyltransferase / Self immunity / resistance / Acetyl coenzyme A | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / nucleotide binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Nair, S.K. / Agarwal, V. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Basis for Microcin C7 Inactivation by the MccE Acetyltransferase. Authors: Agarwal, V. / Metlitskaya, A. / Severinov, K. / Nair, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r9f.cif.gz | 170.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r9f.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 3r9f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/3r9f ftp://data.pdbj.org/pub/pdb/validation_reports/r9/3r9f | HTTPS FTP |
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-Related 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: 21048.295 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mccE / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q47510 #2: Chemical | #3: Chemical | #4: 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: 2.37 Å3/Da / Density % sol: 48.14 % |
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Crystal grow | Temperature: 282 K / Method: hanging drop / pH: 7 Details: PEG550MME, MgCl2, pH 7.0, hanging drop, temperature 282K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 124743 / % possible obs: 99.3 % / Redundancy: 8.6 % / Rmerge(I) obs: 0.065 / Χ2: 1.86 / Net I/σ(I): 12.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→25 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.12 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.043 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.59 Å2 / Biso mean: 16.0726 Å2 / Biso min: 7.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Total num. of bins used: 20
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