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- PDB-4l39: Crystal structure of GH3.12 from Arabidopsis thaliana in complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l39 | ||||||
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Title | Crystal structure of GH3.12 from Arabidopsis thaliana in complex with AMPCPP and salicylate | ||||||
![]() | 4-substituted benzoates-glutamate ligase GH3.12 | ||||||
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Function / homology | ![]() 4-aminobenzoate amino acid synthetase activity / benzoate amino acid synthetase activity / vanillate amino acid synthetase activity / 4-hydroxybenzoate amino acid synthetase activity / salicylic acid mediated signaling pathway / benzoate metabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zubieta, C. / Jez, J.M. / Brown, E. / Marcellin, R. / Kapp, U. / Round, A. / Westfall, C. | ||||||
![]() | ![]() Title: Determination of the GH3.12 protein conformation through HPLC-integrated SAXS measurements combined with X-ray crystallography. Authors: Round, A. / Brown, E. / Marcellin, R. / Kapp, U. / Westfall, C.S. / Jez, J.M. / Zubieta, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 230.5 KB | Display | ![]() |
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PDB format | ![]() | 180.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4epmS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 65762.430 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: GH3.12, GDG1, PBS3, WIN3, At5g13320, T22N19.5, T31B5.140 Production host: ![]() ![]() ![]() References: UniProt: Q9LYU4, ![]() #2: Chemical | ChemComp-MG / | #3: Chemical | ![]() #4: Chemical | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.92 % |
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Crystal grow![]() | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG3350, 0.25 M ammonium acetate, 0.1 M sodium acetate, 5 mM TCEP, 5 mM salicylate, 5 mM AMPCPP, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.81→92.49 Å / Num. all: 28243 / Num. obs: 28172 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.26 / Rsym value: 0.26 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.81→3 Å / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.73 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 4EPM Resolution: 2.81→58.004 Å / SU ML: 0.39 / σ(F): 1.35 / Phase error: 29.17 / Stereochemistry target values: ML Details: RESIDUES FOR THE C-TERMINAL DOMAIN (430-575) WERE MODELED BASED ON PDB ENTRY 4EPM. THESE RESIDUES EXHIBITED HIGH B-FACTORS AND POOR SIDECHAIN AND MAIN CHAIN DENSITY.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→58.004 Å
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Refine LS restraints |
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LS refinement shell |
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