+Open data
-Basic information
Entry | Database: PDB / ID: 2jdc | ||||||
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Title | Glyphosate N-acetyltransferase bound to oxidized COA and sulfate | ||||||
Components | GLYPHOSATE N-ACETYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / GNAT / GLYPHOSATE / N-ACETYLTRANSFERASE | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | BACILLUS LICHENIFORMIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Siehl, D.L. / Castle, L.A. / Gorton, R. / Keenan, R.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: The Molecular Basis of Glyphosate Resistance by an Optimized Microbial Acetyltransferase. Authors: Siehl, D.L. / Castle, L.A. / Gorton, R. / Keenan, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jdc.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jdc.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 2jdc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/2jdc ftp://data.pdbj.org/pub/pdb/validation_reports/jd/2jdc | HTTPS FTP |
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-Related structure data
Related structure data | 2jddC 2bswS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16624.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS LICHENIFORMIS (bacteria) Description: THE ENZYME IS A SHUFFLED VARIANT DERIVED FROM GENES DISCOVERED IN B. LICHENIFORMIS. Plasmid: PQE80 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: Q65LG7*PLUS |
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#2: Chemical | ChemComp-CAO / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
Sequence details | THE N-TERMINAL METHIONINE RESIDUE IS DISORDERED IN THE ELECTRON DENSITY, AND WAS NOT MODELED. ...THE N-TERMINAL METHIONINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % |
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Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE, PH 4.6 150-300 MM AMMONIUM SULFATE 20-25% PEG4000 2 MM ACETYL COA |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0072 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 4, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0072 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32.2 Å / Num. obs: 19217 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 47.9 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 19 / % possible all: 75.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2BSW Resolution: 1.6→32.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.568 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PARTIALLY DISORDERED SURFACE SIDECHAINS WERE MODELED STEREOCHEMICALLY. DISORDERED OR RADIATION DAMAGED SURFACE SIDECHAIN ATOMS WERE MODELED AT 0.5 OCCUPANCY
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.77 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→32.16 Å
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Refine LS restraints |
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