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Yorodumi- PDB-5vd6: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vd6 | ||||||
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Title | Crystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 6 | ||||||
Components | acetyltransferase PA4794 | ||||||
Keywords | transferase/transferase inhibitor / GNAT / acetyltransferase / bisubstrate inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TRANSFERASE / transferase-transferase inhibitor complex | ||||||
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 / molecular replacement / Resolution: 1.2 Å | ||||||
Authors | Majorek, K.A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG) | ||||||
Funding support | United States, 1items
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Citation | Journal: FEBS Lett. / Year: 2017 Title: Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases. Authors: Reidl, C. / Majorek, K.A. / Dang, J. / Tran, D. / Jew, K. / Law, M. / Payne, Y. / Minor, W. / Becker, D.P. / Kuhn, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vd6.cif.gz | 97.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vd6.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vd6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vd6_validation.pdf.gz | 692.1 KB | Display | wwPDB validaton report |
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Full document | 5vd6_full_validation.pdf.gz | 692.2 KB | Display | |
Data in XML | 5vd6_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 5vd6_validation.cif.gz | 16.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/5vd6 ftp://data.pdbj.org/pub/pdb/validation_reports/vd/5vd6 | HTTPS FTP |
-Related structure data
Related structure data | 5vdbC 4l8aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: PA4794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV14 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-93P / ( | #4: 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: 47.74 % |
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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-G / Wavelength: 0.9786 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: Beryllium Lenses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→50 Å / Num. obs: 53381 / % possible obs: 99 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.03 / Rrim(I) all: 0.074 / Χ2: 1.787 / Net I/σ(I): 9.9 / Num. measured all: 325622 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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 Starting model: 4L8A Resolution: 1.2→45.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.162 / WRfactor Rwork: 0.1292 / FOM work R set: 0.9066 / SU B: 1.097 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0348 / SU Rfree: 0.0361 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 89.43 Å2 / Biso mean: 17.654 Å2 / Biso min: 7.9 Å2
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Refinement step | Cycle: final / Resolution: 1.2→45.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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