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Yorodumi- PDB-4oad: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oad | ||||||
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Title | Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with chloramphenicol | ||||||
Components | GNAT superfamily acetyltransferase PA4794 | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / GNAT / acetyltransferase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Majorek, K.A. / Niedzialkowska, E. / Chruszcz, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with chloramphenicol Authors: Majorek, K.A. / Niedzialkowska, E. / Chruszcz, M. / Joachimiak, A. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oad.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oad.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 4oad.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oad ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oad | HTTPS FTP |
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-Related structure data
Related structure data | 4kuaS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 18000.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA4794 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9HV14 | ||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97912 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. all: 31335 / Num. obs: 31335 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 46.9 |
Reflection shell | Resolution: 1.45→1.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1539 / Rsym value: 0.716 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KUA Resolution: 1.45→46 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062 / 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 mean: 23.483 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→46 Å
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