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- PDB-7e13: Caprylic acid targets a serine hydroxymethyltransferase to kill h... -
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Open data
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Basic information
Entry | Database: PDB / ID: 70000000000000 | ||||||
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Title | Caprylic acid targets a serine hydroxymethyltransferase to kill horseweed | ||||||
![]() | serine hydroxymethyltransferase | ||||||
![]() | PLANT PROTEIN / Horseweed / caprylic acid / Serine hydroxymethyltransferase (SHMT) / herbicide target / molecular mechanism | ||||||
Function / homology | PYRIDOXAL-5'-PHOSPHATE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Bai, L.Y. / Li, Z.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: serine hydroxymethyltransferase Authors: Li, Z.R. / Bai, L.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 373.7 KB | Display | ![]() |
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PDB format | ![]() | 306 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 66.4 KB | Display | |
Data in CIF | ![]() | 89.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6smnS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 57072.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 , succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→43.12 Å / Num. obs: 53245 / % possible obs: 98.01 % / Redundancy: 17.9 % / CC1/2: 1 / Rmerge(I) obs: 0.193 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.86→2.96 Å / Rmerge(I) obs: 0.193 / Num. unique obs: 53245 / CC1/2: 1 / Rpim(I) all: 0.04 / Rsym value: 0.139 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6smn Resolution: 2.86→43.12 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 17.869 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / 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: 231.87 Å2 / Biso mean: 78.985 Å2 / Biso min: 30 Å2
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Refinement step | Cycle: final / Resolution: 2.86→43.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→2.934 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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