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Yorodumi- PDB-4oae: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oae | ||||||
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Title | Crystal structure of a GNAT superfamily acetyltransferase PA4794 C29A/C117A/Y128A mutant 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: 1.25 Å | ||||||
Authors | Majorek, K.A. / 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 C29A/C117A/Y128A mutant in complex with chloramphenicol Authors: Majorek, K.A. / 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 | 4oae.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oae.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 4oae.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oae_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4oae_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4oae_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | 4oae_validation.cif.gz | 17.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/4oae ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oae | HTTPS FTP |
-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
#1: Protein | Mass: 17844.375 Da / Num. of mol.: 1 / Mutation: C29A, C117A, Y128A 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: 2.42 Å3/Da / Density % sol: 49.2 % |
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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: 0.91837 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 12, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91837 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. all: 48658 / Num. obs: 48658 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 43.7 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2440 / Rsym value: 0.747 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4KUA Resolution: 1.25→45.96 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.038 / 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: 19.185 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→45.96 Å
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