+Open data
-Basic information
Entry | Database: PDB / ID: 4eql | ||||||
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Title | Crystal Structure of GH3.12 in complex with AMP and salicylate | ||||||
Components | 4-substituted benzoates-glutamate ligase GH3.12 | ||||||
Keywords | LIGASE / firefly luciferase family / acyl adenylase / amino acid conjugation | ||||||
Function / homology | Function and homology information 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 / regulation of systemic acquired resistance / positive regulation of plant-type hypersensitive response / detection of fungus / plant-type hypersensitive response ...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 / regulation of systemic acquired resistance / positive regulation of plant-type hypersensitive response / detection of fungus / plant-type hypersensitive response / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / defense response / cellular response to hypoxia / defense response to bacterium Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Westfall, C. / Zubieta, C. / Nanao, M. / Herrmann, J. / Jez, J. | ||||||
Citation | Journal: Science / Year: 2012 Title: Structural basis for prereceptor modulation of plant hormones by GH3 proteins. Authors: Westfall, C.S. / Zubieta, C. / Herrmann, J. / Kapp, U. / Nanao, M.H. / Jez, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eql.cif.gz | 423.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eql.ent.gz | 341.9 KB | Display | PDB format |
PDBx/mmJSON format | 4eql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eq/4eql ftp://data.pdbj.org/pub/pdb/validation_reports/eq/4eql | HTTPS FTP |
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-Related structure data
Related structure data | 4eplC 4epmC 4eq4SC 4ewvC 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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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.) Arabidopsis thaliana (thale cress) Gene: GH3.12, GDG1, PBS3, WIN3, At5g13320, T22N19.5, T31B5.140 Production host: Escherichia coli (E. coli) References: UniProt: Q9LYU4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | #3: Chemical | #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: 2.26 Å3/Da / Density % sol: 45.59 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 20% PEG3350, 0.25M ammonium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2011 |
Radiation | Monochromator: horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→96 Å / Num. all: 108026 / Num. obs: 106773 / % possible obs: 98.8 % / Observed criterion σ(F): 1.9 / Observed criterion σ(I): 1.9 / Redundancy: 3.7 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.185 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 1.9 / Num. unique all: 17474 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4EQ4 Resolution: 1.8→50.285 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 19.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.986 Å2 / ksol: 0.332 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.8→50.285 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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