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Yorodumi- PDB-5wph: Crystal structure of ArsN, N-acetyltransferase with substrate AST... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wph | ||||||
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Title | Crystal structure of ArsN, N-acetyltransferase with substrate AST from Pseudomonas putida KT2440 | ||||||
Components | Phosphinothricin N-acetyltransferase | ||||||
Keywords | TRANSFERASE / N-acetyltransferase / Pseudomonas putida | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Venkadesh, S. / Dheeman, D.S. / Yoshinaga, M. / Kandavelu, P. / Rosen, B.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Arsinothricin, an arsenic-containing non-proteinogenic amino acid analog of glutamate, is a broad-spectrum antibiotic. Authors: Nadar, V.S. / Chen, J. / Dheeman, D.S. / Galvan, A.E. / Yoshinaga-Sakurai, K. / Kandavelu, P. / Sankaran, B. / Kuramata, M. / Ishikawa, S. / Rosen, B.P. / Yoshinaga, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wph.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wph.ent.gz | 192.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wph_validation.pdf.gz | 491.6 KB | Display | wwPDB validaton report |
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Full document | 5wph_full_validation.pdf.gz | 504.3 KB | Display | |
Data in XML | 5wph_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 5wph_validation.cif.gz | 71.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/5wph ftp://data.pdbj.org/pub/pdb/validation_reports/wp/5wph | HTTPS FTP |
-Related structure data
Related structure data | 5jtfSC 6m7gC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23381.311 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440 / Gene: PP_1924 / Production host: Escherichia coli (E. coli) / References: UniProt: Q88LK7 #2: Chemical | #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 1.5 M Na formate, 0.1 M Na acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→50 Å / Num. obs: 72209 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rpim(I) all: 0.059 / Rrim(I) all: 0.161 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3416 / Rpim(I) all: 0.335 / Rrim(I) all: 0.739 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5JTF Resolution: 2.19→49.02 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.132 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.193
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.029 Å2
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Refinement step | Cycle: 1 / Resolution: 2.19→49.02 Å
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Refine LS restraints |
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