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Open data
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Basic information
Entry | Database: PDB / ID: 3g7d | ||||||
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Title | Native PhpD with Cadmium Atoms | ||||||
![]() | PhpD | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nair, S.K. | ||||||
![]() | ![]() Title: An unusual carbon-carbon bond cleavage reaction during phosphinothricin biosynthesis. Authors: Cicchillo, R.M. / Zhang, H. / Blodgett, J.A. / Whitteck, J.T. / Li, G. / Nair, S.K. / van der Donk, W.A. / Metcalf, W.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.4 KB | Display | ![]() |
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PDB format | ![]() | 77.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 48382.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Phosphinothricin biosynthetic cluster, phpD / Plasmid: pET15 / Production host: ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-CD / #3: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow![]() | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 M sodium acetate, 0.1 M HEPES, 0.05 M cadmium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→50 Å / Num. obs: 36648 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 33.3 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.511 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3480 / % possible all: 90.6 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.698 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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