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Yorodumi- PDB-4klw: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4klw | ||||||
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Title | Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with 2-(aminocarbonyl)benzoate | ||||||
Components | Uncharacterized protein | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG | ||||||
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: 1.3 Å | ||||||
Authors | Majorek, K.A. / Porebski, P.J. / Chruszcz, M. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural, Functional, and Inhibition Studies of a Gcn5-related N-Acetyltransferase (GNAT) Superfamily Protein PA4794: A NEW C-TERMINAL LYSINE PROTEIN ACETYLTRANSFERASE FROM PSEUDOMONAS AERUGINOSA. Authors: Majorek, K.A. / Kuhn, M.L. / Chruszcz, M. / Anderson, W.F. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4klw.cif.gz | 89.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4klw.ent.gz | 66.4 KB | Display | PDB format |
PDBx/mmJSON format | 4klw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4klw_validation.pdf.gz | 457.8 KB | Display | wwPDB validaton report |
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Full document | 4klw_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 4klw_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4klw_validation.cif.gz | 18.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/4klw ftp://data.pdbj.org/pub/pdb/validation_reports/kl/4klw | HTTPS FTP |
-Related structure data
Related structure data | 3pgpC 4klvC 4korC 4kosC 4kotC 4kouC 4kovC 4kowC 4koxC 4koyC 4kuaC 4kubC 4l89C 4l8aC 2i6c C: citing same article (ref.) 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: 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-KLW / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #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: 2.35 Å3/Da / Density % sol: 47.73 % |
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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: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2010 / Details: Beryllium Lenses |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. all: 42231 / Num. obs: 42231 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2 / Num. unique all: 1965 / Rsym value: 0.423 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2i6c 2i6c Resolution: 1.3→32.29 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048 / 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: 20.051 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→32.29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.301→1.335 Å / Total num. of bins used: 20
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