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Yorodumi- PDB-4jxr: Crystal structure of a GNAT superfamily phosphinothricin acetyltr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jxr | ||||||
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Title | Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti in complex with AcCoA | ||||||
Components | Acetyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / GNAT / phosphinothricin acetyltransferase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Sinorhizobium meliloti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.15 Å | ||||||
Authors | Majorek, K.A. / Cooper, D.R. / Porebski, P.J. / Konina, K. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Bonanno, J.B. / Almo, S.C. ...Majorek, K.A. / Cooper, D.R. / Porebski, P.J. / Konina, K. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a GNAT superfamily phosphinothricin acetyltransferase (Pat) from Sinorhizobium meliloti in complex with AcCoA Authors: Majorek, K.A. / Cooper, D.R. / Porebski, P.J. / Konina, K. / Ahmed, M. / Stead, M. / Hillerich, B. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / Minor, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jxr.cif.gz | 198.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jxr.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jxr_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 4jxr_full_validation.pdf.gz | 476.5 KB | Display | |
Data in XML | 4jxr_validation.xml.gz | 24 KB | Display | |
Data in CIF | 4jxr_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/4jxr ftp://data.pdbj.org/pub/pdb/validation_reports/jx/4jxr | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 20477.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: R03223, SMc03840 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL References: UniProt: Q92L60, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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-Non-polymers , 5 types, 703 molecules
#2: Chemical | ChemComp-FLC / |
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#3: Chemical | ChemComp-2PE / |
#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-ACO / |
#6: 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: 2.12 Å3/Da / Density % sol: 42.12 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2 M di-Ammonium citrate pH 5.0, 20% PEG 3350, 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: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2013 / Details: mirrors |
Radiation | Monochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→43.77 Å / Num. all: 122819 / Num. obs: 122819 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 54.7 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.348 / % possible all: 87 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.15→43.77 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.774 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.03 / ESU R Free: 0.03 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 16.457 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→43.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.15→1.18 Å / Total num. of bins used: 20
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